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TRANSCRIPT
2022 Department of Biochemistry and Molecular Biology Student Research Handbook
Handbook for students interested in
bull Research in Action (BCH3990)
bull Honoursbull Masters bull Postgraduate Research
monashedumedicine
Table of Contents
Cell Signalling amp Cancer
Bird Prof Phil 7Cole Prof Tim 9
Mitchell Prof Christina 31Nguyen Dr Lan 33Papa Dr Antonella 35Rosenbluh AProf Joseph 40Tiganis Prof Tony 49Wagstaff Dr Kylie 52Wong AProf Lee 55
Education Research
Samarawickrema Dr Nirma 44
Infection amp Immunity
Bird Prof Phil 7Coulibaly AProf Fasseli 10Croft Dr Nathan 11Davey Dr Martin 13Fletcher Dr Anne 18
Huntington Prof Nicholas 19
Jacobson AProf Kim 21
Jans Prof David 22
Kwok-Schuelein Dr Terry 24
Lahoud Dr Mireille 26Le Nours Dr Jerome 29Mifsud Dr Nicole 30Naderer Dr Thomas 32OrsquoKeeffe AProf Meredith 34Purcell Prof Tony 36Reid Dr Hugh 38Rossjohn Prof Jamie 41Roujeinikova AProf Anna 42Shen Dr Hsin-Hui 46
Tiganis Prof Tony 49Traven Prof Ana 50
Wagstaff Dr Kylie 52Vivian Dr Julian 51
Zaph Prof Colby 56
Illing Dr Patricia 20
Fletcher Dr Anne 18
How to enrol in Honours 4
La Gruta Prof Nicole 25
Stone Prof Martin 48
2
Knott Dr Gavin 23
Genetics amp Development
Beilharz AProf Traude 6Boag Dr Peter 8Cole Prof Tim 9Smyth Prof Ian 47
Molecular Cell Biology
Jans Prof David 22Lazarou Dr Michael 28Ramm AProf Georg 37Ryan Prof Michael 43Schittenhelm AProf Ralf 45
Diabetes amp Obesity
Rose Dr Adam 39Ryan Prof Michael 43Tiganis Prof Tony 49
Structural Biology
Aguilar Prof Mibel 5Coulibaly AProf Fasseli 10Cryle AProf Max 12Davidovich AProf Chen 14De Marco AProf Alex 15Dunstone AProf Michelle 16Ellisdon Dr Andrew 17Law Dr Ruby 27Rossjohn Prof Jamie 41Stone Prof Martin 48Whisstock Prof James 53Wilce Prof Jackie 54Zhang Dr Qi 57
Department of Biochemistry amp Molecular Biology httpswwwmonashedudiscovery-institute
departmentsbiochemistry-and-molecular-biology
3
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3 Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Step 4 Formally apply using eAdmission
Bachelor of Science (dates found at Science Honours landing page)
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3A Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Bachelor of Biomedical Science (dates found at BDI Honours
landing page)
Step 4 Formally apply using eAdmission (This step not required for BMS Advanced with Hons students)
For more information go to httpswwwmonashedudiscovery-institutehonoursso-how-do-i-apply
Step 3B Fill in the online form for BMS (Hons) or the online form for BMS Advanced (Hons)
How to enrol in Honours
4
Biomaterials and Drug Design Professor Mibel AguilarPhone 9905 3723Email mibelaguilarmonashedu httpsresearchmonasheduenpersonsmibel-aguilar
RESEARCH BACKGROUNDOur group focuses on peptide-based drug design and biomembrane nanotechnology We are developing novelcompounds that allow us to exploit the potential of peptides as drugs We are currently applying our technologyto the development of new compounds for treatments of cardiovascular disease and new bio- and nano-materials for tissue engineering and drug delivery Our membrane nanotechnology projects involve studyingthe mechanism of antimicrobial peptide resistance apoptosis and angiotensin receptor function
The long-term aim of these studies is to increase our understanding of the molecular basis of peptide andprotein function and allow the rational design of peptide and protein-based therapeutics
RESEARCH PROJECTS
HONOURSPHD PROJECT 1PEPTIDE-BASED NANOMATERIALSSupramolecular self-assembly represents a powerful approach to the design of functionalnanomaterials in biomedicine and engineering applications Peptide-based materials offer theadvantages of biological compatibility ease of synthesis low toxicity and functionalisabilityThis project involves the design and synthesis of novel self-assembled nano-materials forapplication as novel agents in neuroregeneration wound healing and drug delivery
HONOURSPHD PROJECT 2MECHANISM OF RESISTANCE TO ANTIMICROBIAL PEPTIDESAntibiotic resistance continues to emerge and intensify and while antimicrobial peptides(AMPs) are a promising alternative to current antibiotics bacteria have also evolved a rangeof resistance mechanisms to AMPs which include thickening of the cell wall modification ofthe phospholipid composition changing the net surface charge increasing the membranefluidity releasing proteinases to degrade the peptides and discharging amino acids into theenvironment to reduce hypo-osmotic stress This project aims to characterise how bacteriatransiently modify their lipid content and repel the action of AMPs and how the membranebarrier can be more effectively targeted with agents tailored to lyse compositionally differentmembranes
5
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
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RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
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B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
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Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Table of Contents
Cell Signalling amp Cancer
Bird Prof Phil 7Cole Prof Tim 9
Mitchell Prof Christina 31Nguyen Dr Lan 33Papa Dr Antonella 35Rosenbluh AProf Joseph 40Tiganis Prof Tony 49Wagstaff Dr Kylie 52Wong AProf Lee 55
Education Research
Samarawickrema Dr Nirma 44
Infection amp Immunity
Bird Prof Phil 7Coulibaly AProf Fasseli 10Croft Dr Nathan 11Davey Dr Martin 13Fletcher Dr Anne 18
Huntington Prof Nicholas 19
Jacobson AProf Kim 21
Jans Prof David 22
Kwok-Schuelein Dr Terry 24
Lahoud Dr Mireille 26Le Nours Dr Jerome 29Mifsud Dr Nicole 30Naderer Dr Thomas 32OrsquoKeeffe AProf Meredith 34Purcell Prof Tony 36Reid Dr Hugh 38Rossjohn Prof Jamie 41Roujeinikova AProf Anna 42Shen Dr Hsin-Hui 46
Tiganis Prof Tony 49Traven Prof Ana 50
Wagstaff Dr Kylie 52Vivian Dr Julian 51
Zaph Prof Colby 56
Illing Dr Patricia 20
Fletcher Dr Anne 18
How to enrol in Honours 4
La Gruta Prof Nicole 25
Stone Prof Martin 48
2
Knott Dr Gavin 23
Genetics amp Development
Beilharz AProf Traude 6Boag Dr Peter 8Cole Prof Tim 9Smyth Prof Ian 47
Molecular Cell Biology
Jans Prof David 22Lazarou Dr Michael 28Ramm AProf Georg 37Ryan Prof Michael 43Schittenhelm AProf Ralf 45
Diabetes amp Obesity
Rose Dr Adam 39Ryan Prof Michael 43Tiganis Prof Tony 49
Structural Biology
Aguilar Prof Mibel 5Coulibaly AProf Fasseli 10Cryle AProf Max 12Davidovich AProf Chen 14De Marco AProf Alex 15Dunstone AProf Michelle 16Ellisdon Dr Andrew 17Law Dr Ruby 27Rossjohn Prof Jamie 41Stone Prof Martin 48Whisstock Prof James 53Wilce Prof Jackie 54Zhang Dr Qi 57
Department of Biochemistry amp Molecular Biology httpswwwmonashedudiscovery-institute
departmentsbiochemistry-and-molecular-biology
3
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3 Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Step 4 Formally apply using eAdmission
Bachelor of Science (dates found at Science Honours landing page)
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3A Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Bachelor of Biomedical Science (dates found at BDI Honours
landing page)
Step 4 Formally apply using eAdmission (This step not required for BMS Advanced with Hons students)
For more information go to httpswwwmonashedudiscovery-institutehonoursso-how-do-i-apply
Step 3B Fill in the online form for BMS (Hons) or the online form for BMS Advanced (Hons)
How to enrol in Honours
4
Biomaterials and Drug Design Professor Mibel AguilarPhone 9905 3723Email mibelaguilarmonashedu httpsresearchmonasheduenpersonsmibel-aguilar
RESEARCH BACKGROUNDOur group focuses on peptide-based drug design and biomembrane nanotechnology We are developing novelcompounds that allow us to exploit the potential of peptides as drugs We are currently applying our technologyto the development of new compounds for treatments of cardiovascular disease and new bio- and nano-materials for tissue engineering and drug delivery Our membrane nanotechnology projects involve studyingthe mechanism of antimicrobial peptide resistance apoptosis and angiotensin receptor function
The long-term aim of these studies is to increase our understanding of the molecular basis of peptide andprotein function and allow the rational design of peptide and protein-based therapeutics
RESEARCH PROJECTS
HONOURSPHD PROJECT 1PEPTIDE-BASED NANOMATERIALSSupramolecular self-assembly represents a powerful approach to the design of functionalnanomaterials in biomedicine and engineering applications Peptide-based materials offer theadvantages of biological compatibility ease of synthesis low toxicity and functionalisabilityThis project involves the design and synthesis of novel self-assembled nano-materials forapplication as novel agents in neuroregeneration wound healing and drug delivery
HONOURSPHD PROJECT 2MECHANISM OF RESISTANCE TO ANTIMICROBIAL PEPTIDESAntibiotic resistance continues to emerge and intensify and while antimicrobial peptides(AMPs) are a promising alternative to current antibiotics bacteria have also evolved a rangeof resistance mechanisms to AMPs which include thickening of the cell wall modification ofthe phospholipid composition changing the net surface charge increasing the membranefluidity releasing proteinases to degrade the peptides and discharging amino acids into theenvironment to reduce hypo-osmotic stress This project aims to characterise how bacteriatransiently modify their lipid content and repel the action of AMPs and how the membranebarrier can be more effectively targeted with agents tailored to lyse compositionally differentmembranes
5
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Genetics amp Development
Beilharz AProf Traude 6Boag Dr Peter 8Cole Prof Tim 9Smyth Prof Ian 47
Molecular Cell Biology
Jans Prof David 22Lazarou Dr Michael 28Ramm AProf Georg 37Ryan Prof Michael 43Schittenhelm AProf Ralf 45
Diabetes amp Obesity
Rose Dr Adam 39Ryan Prof Michael 43Tiganis Prof Tony 49
Structural Biology
Aguilar Prof Mibel 5Coulibaly AProf Fasseli 10Cryle AProf Max 12Davidovich AProf Chen 14De Marco AProf Alex 15Dunstone AProf Michelle 16Ellisdon Dr Andrew 17Law Dr Ruby 27Rossjohn Prof Jamie 41Stone Prof Martin 48Whisstock Prof James 53Wilce Prof Jackie 54Zhang Dr Qi 57
Department of Biochemistry amp Molecular Biology httpswwwmonashedudiscovery-institute
departmentsbiochemistry-and-molecular-biology
3
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3 Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Step 4 Formally apply using eAdmission
Bachelor of Science (dates found at Science Honours landing page)
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3A Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Bachelor of Biomedical Science (dates found at BDI Honours
landing page)
Step 4 Formally apply using eAdmission (This step not required for BMS Advanced with Hons students)
For more information go to httpswwwmonashedudiscovery-institutehonoursso-how-do-i-apply
Step 3B Fill in the online form for BMS (Hons) or the online form for BMS Advanced (Hons)
How to enrol in Honours
4
Biomaterials and Drug Design Professor Mibel AguilarPhone 9905 3723Email mibelaguilarmonashedu httpsresearchmonasheduenpersonsmibel-aguilar
RESEARCH BACKGROUNDOur group focuses on peptide-based drug design and biomembrane nanotechnology We are developing novelcompounds that allow us to exploit the potential of peptides as drugs We are currently applying our technologyto the development of new compounds for treatments of cardiovascular disease and new bio- and nano-materials for tissue engineering and drug delivery Our membrane nanotechnology projects involve studyingthe mechanism of antimicrobial peptide resistance apoptosis and angiotensin receptor function
The long-term aim of these studies is to increase our understanding of the molecular basis of peptide andprotein function and allow the rational design of peptide and protein-based therapeutics
RESEARCH PROJECTS
HONOURSPHD PROJECT 1PEPTIDE-BASED NANOMATERIALSSupramolecular self-assembly represents a powerful approach to the design of functionalnanomaterials in biomedicine and engineering applications Peptide-based materials offer theadvantages of biological compatibility ease of synthesis low toxicity and functionalisabilityThis project involves the design and synthesis of novel self-assembled nano-materials forapplication as novel agents in neuroregeneration wound healing and drug delivery
HONOURSPHD PROJECT 2MECHANISM OF RESISTANCE TO ANTIMICROBIAL PEPTIDESAntibiotic resistance continues to emerge and intensify and while antimicrobial peptides(AMPs) are a promising alternative to current antibiotics bacteria have also evolved a rangeof resistance mechanisms to AMPs which include thickening of the cell wall modification ofthe phospholipid composition changing the net surface charge increasing the membranefluidity releasing proteinases to degrade the peptides and discharging amino acids into theenvironment to reduce hypo-osmotic stress This project aims to characterise how bacteriatransiently modify their lipid content and repel the action of AMPs and how the membranebarrier can be more effectively targeted with agents tailored to lyse compositionally differentmembranes
5
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
We recommend a small picture here
Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
We recommend a small picture
here - your photo or
backgrounddata image
Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
We recommend a small picture here -
your photo or backgrounddata
image
Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3 Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Step 4 Formally apply using eAdmission
Bachelor of Science (dates found at Science Honours landing page)
Step 1 Check your third-year marks See if you have an average gt 70 for 24 points in relevant third year subjects or that you are on track to get the marks
If you are not sure contact Michelle (michelledunstonemonashedu)
Step 2 Find a project and supervisor willing to take you on using the Handbook Fill in this enrolment form and get the supervisor to sign
Step 3A Submit enrolment form to the unit coordinatorYou need coordinator approval(michelledunstonemonashedu)
Bachelor of Biomedical Science (dates found at BDI Honours
landing page)
Step 4 Formally apply using eAdmission (This step not required for BMS Advanced with Hons students)
For more information go to httpswwwmonashedudiscovery-institutehonoursso-how-do-i-apply
Step 3B Fill in the online form for BMS (Hons) or the online form for BMS Advanced (Hons)
How to enrol in Honours
4
Biomaterials and Drug Design Professor Mibel AguilarPhone 9905 3723Email mibelaguilarmonashedu httpsresearchmonasheduenpersonsmibel-aguilar
RESEARCH BACKGROUNDOur group focuses on peptide-based drug design and biomembrane nanotechnology We are developing novelcompounds that allow us to exploit the potential of peptides as drugs We are currently applying our technologyto the development of new compounds for treatments of cardiovascular disease and new bio- and nano-materials for tissue engineering and drug delivery Our membrane nanotechnology projects involve studyingthe mechanism of antimicrobial peptide resistance apoptosis and angiotensin receptor function
The long-term aim of these studies is to increase our understanding of the molecular basis of peptide andprotein function and allow the rational design of peptide and protein-based therapeutics
RESEARCH PROJECTS
HONOURSPHD PROJECT 1PEPTIDE-BASED NANOMATERIALSSupramolecular self-assembly represents a powerful approach to the design of functionalnanomaterials in biomedicine and engineering applications Peptide-based materials offer theadvantages of biological compatibility ease of synthesis low toxicity and functionalisabilityThis project involves the design and synthesis of novel self-assembled nano-materials forapplication as novel agents in neuroregeneration wound healing and drug delivery
HONOURSPHD PROJECT 2MECHANISM OF RESISTANCE TO ANTIMICROBIAL PEPTIDESAntibiotic resistance continues to emerge and intensify and while antimicrobial peptides(AMPs) are a promising alternative to current antibiotics bacteria have also evolved a rangeof resistance mechanisms to AMPs which include thickening of the cell wall modification ofthe phospholipid composition changing the net surface charge increasing the membranefluidity releasing proteinases to degrade the peptides and discharging amino acids into theenvironment to reduce hypo-osmotic stress This project aims to characterise how bacteriatransiently modify their lipid content and repel the action of AMPs and how the membranebarrier can be more effectively targeted with agents tailored to lyse compositionally differentmembranes
5
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
We recommend a small picture here
Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Biomaterials and Drug Design Professor Mibel AguilarPhone 9905 3723Email mibelaguilarmonashedu httpsresearchmonasheduenpersonsmibel-aguilar
RESEARCH BACKGROUNDOur group focuses on peptide-based drug design and biomembrane nanotechnology We are developing novelcompounds that allow us to exploit the potential of peptides as drugs We are currently applying our technologyto the development of new compounds for treatments of cardiovascular disease and new bio- and nano-materials for tissue engineering and drug delivery Our membrane nanotechnology projects involve studyingthe mechanism of antimicrobial peptide resistance apoptosis and angiotensin receptor function
The long-term aim of these studies is to increase our understanding of the molecular basis of peptide andprotein function and allow the rational design of peptide and protein-based therapeutics
RESEARCH PROJECTS
HONOURSPHD PROJECT 1PEPTIDE-BASED NANOMATERIALSSupramolecular self-assembly represents a powerful approach to the design of functionalnanomaterials in biomedicine and engineering applications Peptide-based materials offer theadvantages of biological compatibility ease of synthesis low toxicity and functionalisabilityThis project involves the design and synthesis of novel self-assembled nano-materials forapplication as novel agents in neuroregeneration wound healing and drug delivery
HONOURSPHD PROJECT 2MECHANISM OF RESISTANCE TO ANTIMICROBIAL PEPTIDESAntibiotic resistance continues to emerge and intensify and while antimicrobial peptides(AMPs) are a promising alternative to current antibiotics bacteria have also evolved a rangeof resistance mechanisms to AMPs which include thickening of the cell wall modification ofthe phospholipid composition changing the net surface charge increasing the membranefluidity releasing proteinases to degrade the peptides and discharging amino acids into theenvironment to reduce hypo-osmotic stress This project aims to characterise how bacteriatransiently modify their lipid content and repel the action of AMPs and how the membranebarrier can be more effectively targeted with agents tailored to lyse compositionally differentmembranes
5
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
RNA Systems BiologyAssociate Professor Traude BeilharzPhone 9902 9183 Email traudebeilharzmonashedu httpswwwmonashedudiscovery-institutebeilharz-lab
RESEARCH BACKGROUND
As demonstrated first by CRISPR and now mRNA vaccines RNA technologies are set to be disruptive new medicines The lab studies RNA metabolism the birth life and death of RNA molecules motivated by a conviction that through the combined use of next-generation technologies and evolutionary conservation in model organisms we can significantly accelerate the discovery of gene functions With the advent of personal genomic medicine a detailed understanding of gene function has never been more critical In the future regular ldquoomicsrdquo measurements overlaid on our genomes might be the norm Each of us carries numerous ldquodiseaserdquo mutations and countless further genetic variations mostly unknown consequences Skills in advanced genomics will be critical future assets
The RNA-systems laboratory makes extensive use of RNA-seq traditional wet-lab methodologies and computational approaches Interested applicants can customise the projects below to best suit their interests Students with computational backgrounds are especially encouraged to make contact as this is a significant growth area of the future
HONOURS PROJECTSPROJECT 1 Uncovering the function of alternative polyadenylation RNA is a remarkable molecule in that it has structural catalytic and information encoding capability Yet how these properties are programmed is still largely mysterious More than 75 of mRNA can have alternative 3 Untranslated Regions (3UTRs) and shortening correlates to disease where a change in 3UTR usage creates significant scope for post-transcriptional regulation This project concerns the consequence that 3UTR isoforms switching has on the efficiency of protein translation
PROJECT 2 Investigating the switch from translational silence to activation The poly(A)-tail that terminates mRNA is modified in the cytoplasm to regulate protein translation where lengthening activates translation and poly(A)-trimming results in silencing Such tuning of gene expression by poly(A)-length change is essential in the brain and germline and is misregulated in disease However the enzymes responsible for this cytoplasmic polyadenylation are unclear therefore a systematic analysis of poly(A)-polymerases is urgently needed Projects are available in the male and female mouse germline
PROJECT 3 Bioinformatic investigation of biosynthetic gene clusters in fungal genomes Biosynthetic gene clusters are found in many fungal species and represent information to make some of our most essential medicines such as statins antibiotics and anticancer drugs Australia has among the most diverse fungal species on the planet but only a small proportion have been sequenced or bioinformatically analysed for bioactive compounds Therefore the project will use machine learning other computational tools to mine in-house and public data in search of gene pathways that encode possibly valuable compounds
6
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
We recommend a small picture
here - your photo or
backgrounddata image
Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
We recommend a small picture here -
your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
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Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Cell Development and DeathProfessor Phillip BirdPhone 03 99029365 Email philbirdmonasheduhttpswwwmonashedudiscovery-institutebird-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Serpins and cell deathSerpins are proteins that trap and inactivate proteases and are present inside cells (intracellular) and in thecirculation (extracellular) Some intracellular serpins protect cells against injury by their own proteasesSerpin deficiency or misfolding in humans results in blood clots immune dysfunction lung and liver diseasecancer or dementia
1 SerpinA1 is an extracellular protein produced in the liver andreleased into the circulation to protect the lung from neutrophilproteases Mutation and misfolding of SerpinA1 results in thefailure of hepatocytes to release it into the circulation and theretained protein aggregates in the ER leading to hepatocytedeath and resulting in liver and lung disease To study thisprocess we have made transgenic zebrafish expressing wildtype or mutant human SerpinA1 (Fig 1) Proteomic andtranscriptomic analyses have identified metabolic pathwaysperturbed in fish expressing mutant SerpinA1 Current studiesare aimed at manipulating key genes in these pathways toameliorate serpin misfolding and increase its release andidentify targets for human therapeutic development Zebrafishprojects are co-supervised by AProf R Bryson-Richardson(School of Biological Sciences)
2 Serpinb6 is an intracellular serpin produced by leukocytesand epithelial cells Surprisingly mutation of Serpinb6 causesadult-onset hearing loss in humans Using knockout mice wehave shown that Serpinb6 deficiency causes inner eardegeneration hair cell death and hearing loss (Fig 2) We thinkthat the hearing loss seen in Serpinb6-deficient individualsresults from failure to protect cells of the inner ear from aprotease released by noise trauma We wish to identify theprotease its location and produce antibodies that inhibit it
In these studies we use advanced techniques in molecular cellbiology These include recombinant protein production andanalysis gene manipulation RNA interference proteomicstranscriptomics bioinformatics cell culture and confocalimaging and the analysis of model organisms
Fig 1 Transgenic zebrafish expressing GFP and SerpinA1 in hepatocytes
Fig 2 Loss of hair cells in cochlea of an adult Serpinb6 KO mouse
7
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Developmental and RNA Biology LabDr Peter BoagPhone 9902 9117Email peterboagmonasheduhttpswwwmonashedudiscovery-instituteboag-lab
RESEARCH BACKGROUNDThe Boag lab is interested in how gene expression is regulated at the RNA level The genome of all eukaryote organisms contains hundreds of RNA-binding proteins that control the fate of the diverse and distinct classes of RNA found within the cell Although these RNA-binding proteins proved a key layer in coordinating gene expression programs the function of most of these proteins remains unknown Interestingly many RNA-binding proteins are concentrated in membrane-less organellesgranules in the cytoplasm of the cell How these membrane-less organellesgranules form is only now beginning to be investigated at a molecular level Our lab uses germ granules as a model to investigate RNA-proteins granule formation and dynamics and uses a combination of biochemical cell biology genetic and genomic technologies
HONOURS PROJECTS Project 1 Transgenerational Epigenetic inheritance C elegans is at the forefront of understanding small RNA biology and has been a platform upon whichmany paradigm-shifting concepts have emerged Using this system we are investigating proteins that arerequired for normal functions of small RNA pathways required for maintaining the epigenetic landscape ofthe genome We have an honours project that will investigate a novel RNA-binding protein that is requiredfor small RNA-mediated maintenance of the epigenetic organisation of the genome across generations
Project 2 The role of RNA-proteins granules in regulating gene expressionLarge RNA-proteins granules are an evolutionarily conserved feature of germ cells and play a key role in regulating gene expression These granules have liquid-like properties and appear to form by a process called liquid-liquid phase separation We are interested in examining a conserved RNA-protein complex that localises to germ granules and is required for translational regulation of selected mRNAs This project will investigate the connection between liquid-liquid phase separation RNA-protein complex formation and translational repression
8
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Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
We recommend a small picture here
Endocrine Signalling amp DiseaseProfessor Tim ColePhone 9905 9118 Email timcolemonashedu httpswwwmonashedudiscovery-institutecole-lab
RESEARCH PROJECT BACKGROUNDThe endocrine system controls cell-cell communication and coordinates almost all our daily activities Abnormalities in hormones receptors and cell signalling pathways underpin many common diseases such as cancer diabetes high blood pressure and obesity We are studying the actions of two important adrenal steroid hormones cortisol (a glucocorticoid) and aldosterone (a mineralocorticoid) that are secreted by the adrenal gland and regulate important aspects of systemic physiology and homeostasis in humans and other mammals Cortisol has many homeostatic roles in a wide range of tissues both during embryogenesis particularly the developing lung Premature babies have underdeveloped lungs and require treatment with synthetic glucocorticoids Glucocorticoids exert their effects by binding to the intracellular glucocorticoid and mineralocorticoid receptors GR and MR respectively Both are members of the nuclear receptor super-family of ligand-dependent nuclear transcriptional regulators Research projects below will utilize a range of molecular biochemical and genetic techniques in both cell-based and animal systems to investigate these cell signalling pathways and their specific roles
2022 HONOURS PROJECTS1 Glucocorticoid-regulated pathways in the preterm lung and testing SelectiveGlucocorticoid Receptor (GR) Modulators (SGRMs) Lung dysfunction in adults and frompremature birth is a major cause of morbidity and mortality Systemic hormones such as retinoic acid glucocorticoids play an important role in embryonic lung development We have a number of mouse gene-knockouts that interrupt the cell signalling of these hormones These include mouse knockout lines of the GR MR and HSD1 genes GR-null mice develop perinatal lung dysfunction and will be used to investigate the specific molecular and cellular role each hormonereceptor pathway plays during fetal respiratory development We are utilizing the Cre-recombinaseloxP gene recombination system in mice to produce cell-type-specific gene knockouts in the developing lung This will identify specific endocrine actions of these pathways in mesenchymal epithelial and endothelial cell compartments Novel steroid-like compounds are being developed that have potent selective effects via the GR in specific tissues such as the liver brain and respiratory system These compounds bind to the GR and modulate interactions in the nucleus of cells to allow regulation of particular sets of down-stream target genes This aspect of the project will test a range of new SGRM compounds in lung cell lines lung explants cultures and in vivo with mice for potential clinical use
2 The Short-Chain Dehydrogenase Reductase (SDR) Enzymes Roles in metabolismand cancer This project will investigate SDR enzymes such as 11bHSD31L a third member of the 11bHSDenzyme sub-family This enzyme is absent in rodents and we will study its expression pattern in tissues cellular localisation using specific antibodies and substrate specificity in samples from non-human primates the sheep and in available human tissue samples and human cell lines3 Novel Roles of Mineralocorticoid Receptor (MR) Signalling in vivoThe adrenal steroid aldosterone regulates systemic fluid and solute homeostasis in the kidneydistal colon via
genomic actions in the nucleus via the activated MR We have made novel tissue-specific mouse knockouts of the MR and also both dimerization and LBD mouse mutants to explore novel genomic amp non-genomic actions in non-epithelial cellstissues such as macrophages cardiomyocytes vascular endothelial cells the lung and specialised neurones in the brain (in collaboration with Prof Peter Fuller MIMR-PHI Clayton and AProf Morag Young The Baker-IDI Institute Prahran)
9
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
We recommend a small picture
here - your photo or
backgrounddata image
Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
We recommend a small picture here -
your photo or backgrounddata
image
Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
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Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Structural VirologyAssociate Professor Fasseli CoulibalyPhone 03 990 29225 Email fasselicoulibalymonasheduwwwmonashedudiscovery-institutecoulibaly-lab
RESEARCH BACKGROUND
HONOURS PROJECTSPhage infecting Salmonella Typhi(X-ray crystallography amp cryo-EM)
The Structural Virology laboratory aims at understanding the assembly and replication of virusescombining molecular virology and structural biology approaches Our research produces 3-D molecularmodels of viruses and viral proteins to provide functional insights and design novel antiviral therapeutics
Projects1- Structure determination and engineering of beneficial viruses2- Using chimeric viruses for structural vaccinology againstmosquito-borne viruses
Structure determination and engineering of beneficial virusesViruses are best known for the diseases they cause in human animals and plants This historical focus ona limited number of pathogenic viruses has occulted for long the fact that most viruses do not causedisease in animals and plants Indeed life thrives despite ndash or perhaps thanks to ndash staggering numbers ofviruses which outnumber cellular organisms by an order of magnitude Thus viruses represent aformidable evolutionary force as vectors of genetic exchange and constant selective pressure This is trueat every scales from the microbiota in our guts to the microbial communities in large ecosystems suchas seas and oceans This provocative view of viruses led to the recognition that some of them could beour allies in research biotechnology and health
This project will investigate the structure and function of viruses that have novel applications to humanhealth as vaccines antimicrobial agents (ie phage therapy) and production systems for therapeuticsDespite the beneficial impact and biomedical potential of these viruses their engineering has beenimpeded by the lack of molecular understanding of essential processes specifically the self-assembly ofthe viral capsid and its trafficking inout of the cell The Honours project will aim at filling this gap by (i)generating 3D model of the infectious particle using integrated structural biology approaches and (ii)elucidating key aspects of viral assembly using in vitro assembly assays and imaging
Fields of research molecular virology structural biology biochemistry immunology (vaccine)
Techniques molecular biology (cloning site-directed mutagenesis) protein biochemistry (proteinexpression amp purification biophysical characterisation) and structural biology (X-ray crystallography cryo-EM) Computational aspects can be performed if access to the laboratory is restricted (protein modelling)
PMC7385642 (2020 Nature Commun) PMC81231421 (2021 Science Advances) PMC8169900 (2021 Nature Commun)
Do not hesitate to contact me for further details on either project (fasselicoulibalymonashedu) 10
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Systems Immunology GroupDr Nathan CroftPhone 03 9902 0473 Email nathancroftmonasheduwwwmonashedudiscovery-institutecroft-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
My research is focused on understanding how different aspects of the MHC antigen processingpathway impact upon T cell immunity to pathogens and tumors I am particularly interested in howthe abundance of MHC-bound peptides plays a role in driving the magnitude and efficacy of T cellresponses The Systems Immunology Group utilises a combination of biochemistry immunologyproteomics and bioinformatics to take a holistic view of immune processes striving to developnovel bioinformatics and data repositories that will model and predict the generation of peptideepitopes and their immunogenicity The Systems Immunology Group is part of the largerImmunoproteomics Laboratory (led by Prof Tony Purcell) specialising in using cutting-edge massspectrometry instrumentation to study MHC-peptide repertoires (collectively termedimmunopeptidomes) Our recent publications include characterization of peptide presentationdriving T cell responses to vaccinia virus [1] and influenza virus [2] refining our understanding ofpeptide splicing [3] and investigating the role of post-translational deamidation as a hallmark ofprior protein glycosylation [4]
References1 Croft et al (2019) Proc Natl Acad Sci U S A [PMID 30718433]2 Wu et al (2019) Nat Commun [PMID 31253788]3 Faridi et al (2018) Sci Immunol [PMID 30315122]4 Mei et al (2020) Mol Cell Proteomics [PMID 32357974]
A number of projects are available although these may initially be limited to computationalprojects (2)Project 1 Does the immune system have a sweet toothThe presentation of post-translationally modified (PTM) peptides by cell surface MHC moleculesincreases the diversity of targets for recognition by T cells Currently little is known as to how theimmune system handles the addition of sugars (glycosylation) to proteins and whether glycosylatedpeptides are presented to T cells This project will combine immunology and glycobiology (incollaboration with Prof Anthony Purcell at Monash and Dr Morten Thaysen Andersen at MacquarieUniversity) to better understand how the immune system monitors protein glycosylationProject 2 Interrogating immunopeptidomes through data visualisationThis project seeks to develop and apply innovative methods of bioinformatics and data visualizationto dig deeper into vast immunopeptidomics datasets Candidates should have experience in codingand a willingness to apply creative thinking to problem solvingProject 3 Defining the role of ubiquitination in antigen presentationProtein degradation by the proteasome is critical for peptide presentation to T cells yet the extentto which this is dependent upon ubiquitination is poorly understood This project will address thisthrough biochemical methods employing a newly characterized inhibitor of ubiquitination andassessment of immunopeptidomes by mass spectrometry
11
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Antibiotic Biosynthesis amp Development Associate Professor Max CrylePhone 99050771 Email maxcrylemonasheduwwwmonashedudiscovery-institutecryle-lab
RESEARCH BACKGROUNDMy group investigates two main topics the biosynthesis of the glycopeptide antibiotics (GPA) and the development of novel antibiotics to treat serious bacterial pathogens GPAs include vancomycin and their natural biosynthesis remains the only route to their commercial production by studying and understanding GPA biosynthesis we aim to identify new more effective antibiotics and how to produce them We also develop new antimicrobial therapies against multi-drug resistant Staphylococcus aureus that exploit a combined immuneantibiotic approach Our projects are multi-disciplinary supported by our expertise in chemical synthesis X-ray crystallography enzymatic catalysis amp protein engineering
HONOURS PROJECTSProject 1 Combining immune recruitment with antibiotics to kill Golden Staph ndash antibiotics haveundoubtedly improved life expectancy and underpin modern medicine however increasing resistancemeans that society is badly in need of new approaches to treat antibiotic resistant bacterial infections Inthis project you will explore combinations of a clinical antibiotic and innate immunity peptides thatrecruit the immune system to target and treat bacterial infections This will involve generating modifiedantibiotics testing their activity against clinically relevant isolates of the superbug Staphylococcus aureus(Golden Staph) and assessing the immune recruitment effects of antimicrobial peptides on neutrophilsthe immune systems ldquofirst respondersrdquo involved in fighting bacterial infections
Project 2 Structural and biochemical characterisation of an unusual peptide antibiotic producingassembly line ndash non-ribosomal peptide synthetases (NRPSs) are amazing peptide assembly lines thatproduce highly modified and bioactive peptides Antibiotics are without doubt one of the mostimportant classes of natural product and many are produced by NRPS assembly lines Whilst themodular architecture of most NRPSs is conceptually well understood we known comparatively littleabout the structure of complete multi-modular assembly lines In this project you will reconstitute anunusual NRPS machinery characterise the behaviour of this machinery in vitro and structurallycharacterise the assembly line using cryo-electron microscopy (Cryo-EM)
Project 3 Engineering the biosynthesis of peptide antibiotics via enzyme redesign ndash many peptideantibiotics including the glycopeptide antibiotics are produced by a non-ribosomal peptide synthesis Akey domain in the biosynthesis of such peptides are adenylation (A) domains which are responsible forthe selection and activation of each amino acid building block In this project you will design produceand characterise variants of the adenylation domains responsible for incorporating unusual amino acidsinto the glycopeptide antibiotics in terms of their structure and function
12
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Immune Surveillance GroupDr Martin DaveyARC DECRA FellowPhone 99050255 Email martindaveymonasheduwwwmonashedudiscovery-institutedavey-lab
RESEARCH BACKGROUNDThe adaptive arm of immune system useslymphocytes to generate antibody andmemory responses to challenges throughoutlife Three lineages of lymphocytes have co-evolved over the last 550 million years Bcells ɑβ T cells and γδ T cells Human γδ Tcells remain poorly understood and theirexact role in immunity is unclear Howeverhuman γδ T cells are frequently implicated inprotective microbial and tumour immunity γδT cells are distributed throughout the bodyand form an extensive immune surveillancenetwork (Figure 1) Our group seeks toexplore the role of this network in health anddisease
Project 1 γδ T cell memory responses intuberculosis infection Tuberculosis is causedby an infection with the bacterial pathogenMycobacterium tuberculosis (Mtb) Despitesignificant efforts to control and eliminate Mtb it remains a significant global health problem 90 of acuteMtb infections results in a state of latent Mtb The student will use 17-colour flow cytometry antibody panelsto track the emergence of anti-Mtb γδ T cell responses in longitudinal blood samples from patients eitheracutely or latently infected with Mtb The student will then sort γδ T cell subsets and perform cutting-edgeγδTCR repertoire sequencing to understand the TCR response to this pathogen
HONOURS PROJECTS
Project 2 Transcriptional control of γδ T cells in CMV infection Cytomegalovirus (CMV) is a humanherpesvirus that infects over 80 of the population and is a major cause of mortality in immunocompromisedindividuals γδ T cells make a dramatic and sustained expansion towards acute CMV infection in transplantpatients the magnitude of which has been correlated with lower morbidity and transplant failure Thestudent will have access to longitudinal cohorts undergoing CMV activation in different transplant scenarios(lung kidney and stem cell) The student will undertake state-of-the-art single cell RNA sequencing to mapthe transcriptional trajectories of CMV-reactive γδTCRs in stem cell transplant patients
Project 3 Human intestinal γδ T cells in inflammation Human γδ T cells are enriched at intestinal barriersites where microbial infection and chronic inflammation occur The student will have access to paediatricintestinal biopsies on a weekly basis from Monash Childrenrsquos Hospital The student will use state-of-the-artsingle cell TCR sequencing and RNAseq to investigate matched blood and tissue samples allowing theidentification of tissue resident γδ T cell populations Understanding the properties of these tissue residentsentinels will allow the development of new γδ T-cell-based immunotherapeutics
Figure 1 The circulating repertoire of γδ T cells is formed of both naiumlve and effector subsets Each subset preferentially localises to the peripheral (effector) and lymphoid (naiumlve) tissues
13
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Epigenetic Regulation Structure and Function Associate Professor Chen DavidovichPhone 9905 5702 Email chendavidovichmonashedu wwwdavidovich-labcom
HONOURS PROJECTSProject 1 Synthetic biology meets epigenetics What I cannot create I do notunderstand (Richard Feynman) For a mechanistic study of epigenetic repression thisentire process is reconstituted in the test tube or model organisms Structure-functionstudies using reconstituted systems are carried out using high-resolution cryo-EM X-raycrystallography electron cryotomography mass spectrometry-based proteomics to mapproteinndashprotein proteinndashDNA and proteinndashRNA interactions and next-generationsequencing-based approaches to detect molecular interactions and enzymatic activity
Project 3 Epigenetic regulation of oncogenes and developmentally expressed genes Themolecular mechanism of gene repression and derepression (activation) will be identifiedthrough the utilization of genome editing techniques (CRISPR-Cas9) combined withproteomic approaches next-generation sequencing techniques and genetic screens
How genes are turned off and then maintained repressed throughout countless cell divisions Theprocess of maintaining genes in a repressed state requires chromatin modifiers enzymes that modifyhistone proteins and DNA at the immediate vicinity of repressed genes The modified chromatin isthen maintained in a compacted and repressed state throughout countless of cell division in aprocess often refers to as epigenetic repression We wish to understand how chromatin-modifyingcomplexes maintain the repressed state of genes at the molecular levelChromatin modifiers are dysregulated in most types of cancer leading to the expression ofoncogenes and the repression of tumour
Project 2 Develop a platform for drug screens to target epigenetic modifiers in cancerThe project will aim to develop assays and approaches to identify selective inhibitors totarget specific type(s) of epigenetic modifiers in specific contexts The project will set thefoundation for the development of a platform to screen for highly specific drugs selectivelytargeting subtypes of epigenetic modifiers in a defined genetic and epigenetic context(s) Inthe long run the project will allow for the development of precision epigenetic therapiesaiming for personalised medicine
suppressor genes Therefore chromatinmodifiers are considered as promisingdrug targets and there is a large interestto understand how they are regulated atthe molecular level The Davidovich labutilises cutting edge approaches instructural biology biochemistry and cellbiology in order to determine howchromatin modifiers are regulated at themolecular level
REASEARCH BACKGROUND
14
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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your photo or backgrounddata
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
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Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
Technology development for in situ structural biologyAssociate Professor Alex de MarcoPhone 9905 3791 Email alexdemarcomonasheduhttpswwwmonashedudiscovery-institutede-marco-lab
HONOURS PROJECTS
Biological systems are extremely complex and dynamic Over the past 10 years there has been an explosion of technical advancements in both and Electron Microscopy Those advancements led to the possibility to obtain structural information about any protein directly while still within their natural environment the cell
Development of cryo-correlative FIB millingThrough the use of correlative microscopy it is possible to identify any event in a cell study its dynamics and resolve the structural conformation In my lab we are developing an ultra-stable cryo-light microscope that will be able to perform super-resolution imaging on cryopreserved samples We will use the information retrieved through this imaging technique to drive the isolation of regions of interest through cryoFIB milling Those regions will be then imaged using cryo-Electron Tomography The project will need some basic coding capabilities
Development of fast super-resolution Light Sheet MicroscopySuper resolution light microscopy is an extremely powerful tool in cell biology unfortunately it is limited by either its time resolution or the photon dose required which can be phototoxic We will combine structured illumination and the use of a light-sheet in order to obtain fast and low-dose super-resolution light microscopyThe project will involve ray-tracing and design of optical systems
All projects are conducted in the framework of the ARC centre of Excellence for Molecular Imaging The first two are adequate for a student with a background in physics and interest in Optics The third project would de suitable for a student with a background in Chemistry and interested in Organic and Analytical Chemistry
RESEARCH BACKGROUND
15
Bacterial toxins and Immunity LabAssociate Professor Michelle DunstonePhone 9902 9269Email michelledunstonemonasheduhttpswwwmonashedudiscovery-institutedunstone-lab
RESEARCH BACKGROUND
Using immune system hole-punching proteins to fight inflammation and cancerThe Membrane Attack Complex (MAC) is a giant hole-punching complex that targets and kills invadingbacteria and parasites Insufficient MAC leads tosusceptibility to bacterial infection Too much MACassembly leads to unwanted inflammation Currentlywe do not understand how the MAC assembles onthe target membrane or how it is inhibited by CD59
HONOURS PROJECTS
Pore forming toxins (PFTs) are fascinating proteins have the ability to breach cell membranes by formingpores in the lipid bilayer These pores can be either lytic to the target cell eg by osmotic flux or thepores can mediate the translocation of toxic proteins into the target cell They are found in all kingdomsof life especially pathogenic bacteria My research looks at the structure and evolution of pore formingtoxins such as the MAC fungal toxins and aerolysin PFTs are being developed for Third GenerationSequencing biosensors and pest control in agriculture
Pore forming toxins in agriculture and biosecurityPore forming toxins are used in Australian cotton and canola crops to convey resistance to specific insect pests and reduce the dependence on chemical pesticides However there is emerging resistance in insect populations to the actions of these toxins Nematodes can also be an issue in optimal growth of crops We are working on several new pore forming toxins that are insecticidal or nematocidal that can be used to enhance the resistance of crops to insects and nematodes
This study of MAC will tell exactly how the MAC changes shape to punch into the membrane and how wecan stop this hole-punching action in inflammation or to fight cancer This will include the use of highresolution techniques including Single Particle-cryo Electron Microscopy and cryo-Electron Tomography
Pore forming proteins in nanotechnologyPore forming proteins in the lab will be used to develop a ldquoproof ofconceptrdquo experiment to test if MACPFCDC pore forming toxins canbe used in electrophysiology sensing Electrophysiology sensing canbe applied to develop biosensors or third generation sequencing(TSG) Collaboration with Oxford Nanopore Technologies (UK)
16
Structural Biology of Signalling and Cancer LaboratoryDr Andrew EllisdonEmail andrewellisdonmonashedu httpswwwmonashedudiscovery-instituteellisdon-lab
RESEARCH BACKGROUNDAlterations in the finely tuned balance of signalling pathways underlie the pathogenesis of a host ofdiseases from cancer to inflammation Capturing an atomic view of lsquosignaling in actionrsquo by determiningthe structures of key signaling components is central to the development of targeted therapeuticsThe laboratoryrsquos research vision is to determine structures of critical multi-component proteincomplexes formed by tumour-suppressor proteins and oncogenes This resolution is enabled bycombining the latest advances in single-particle cryoEM and crystallography with advanced single-cellfluorescence techniques Importantly the incorporation of proteins into signalling complexes oftenreveals unique sites that can be therapeutically exploited to both increase specificity of medicines anddecrease unwanted lsquoon targetrsquo side effects In parallel the team has a long-term aim to translate keymechanistic findings on the anti-inflammatory signalling of IL-1 family cytokines to the clinic
HONOURS PROJECTSProject 1 IL-1 family receptors in inflammationInterleukin-1 (IL-1) family cytokines play key roles in the initiation and regulation of innate immunityand inflammation In 2015 Dr Ellisdon (BDI) and Prof Whisstock (BDI) formed a collaboration with AProf M Nold and Dr C Nold (Hudson Institute) to translate the anti-inflammatory activity of IL-1family cytokines to the clinic Publications from the collaboration include studies in ScienceImmunology (Ellisdon et al 2017) and Nature Immunology (Nold-Petry et al 2015) Current projectsinclude harnessing X-ray crystallography to understand the structural basis of IL-1 receptor signallingin inflammationProject 2 CryoEM and crystallography of GEF and GAPcomplexes in cancerRhoGTPases are small G protein members of the Rassuperfamily that regulate cytoskeletal organization cell-cycle progression and gene expression and theirdysregulation drives tumourigenesis and metastaticdissemination Guanine-nucleotide-exchange factors(GEFs) turn on signalling by catalysing the exchange ofGDP for GTP on target G-proteins whereas GTPase-activating proteins (GAPs) terminate signalling bypromoting GTP hydrolysisCurrent projects include characterisation of the activation of the metastatic factor and GEF P-Rex1 atthe plasma membrane by Gβγ gaining a mechanistic understanding of the inhibitory complex formedbetween the tumour-suppressor protein PTEN and the oncogenic GEF P-Rex2 and determining thefirst architectural insights into the complete tuberous sclerosis complex (TSC)
17
STROMAL IMMUNOLOGY LABDr Anne FletcherPhone 03 9905 1743 Email AnneLFletchermonasheduhttpsresearchmonasheduenpersonsanne-fletcher
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Cancer-associated fibroblasts (CAFs) are the most important tumour cells yoursquove never heard of Theseabundant structural cells are not themselves cancerous but they expand within the tumour (see ourhuman colorectal images below) and directly influence whether or not patients respond to chemotherapyand immunotherapy We are exploring how tumour fibroblasts influence the anti-tumour immuneresponse which is an exciting and clinically relevant topic at the forefront of cancer research The CAF loadin a tumour strongly predicts poor outcomes for patients and in many tumours CAFs even outnumbertumour cells yet our understanding of their function is still in its infancy Our new work shows that humanCAFs directly impair anti-tumour T cell activation and we are working towards development of a new classof anti-cancer drugs that target CAFs Our lab is passionate hard-working creative collaborative andfunded through a mix of academic and industry sources creating a range of opportunities depending onyour interests Irsquom an experienced honours supervisor who is enthusiastic about your career developmentwherever you are headed and I have strong experience in supporting students to build their CV so they arecompetitive for PhD scholarships A strong focus in cell biology or Immunology is an advantage
We recently made novel immortalized fibroblast cell lines from humantumours These express Cas9 for CRISPR knockouts as well asfluorescent markers and we suddenly have more exciting knockouts tolook at than people to study them so we are looking for a talentedstudent to select one or more genes of interest validate the knockoutand explore its function including making downstream CRISPRknockouts where relevant The projects are flexible but designed tomaximise the chance of generating interesting publishable outcomesProject 1 How do CAFs interfere with anti-tumour immunity Usinghuman cell cultures and mouse models of cancer a candidate gene willbe chosen and tested for its function in CAFs Candidates includeTGFBRI and II COX2 CSF1 FAP or others Experimental approachesinclude imaging and flow cytometry use of blocking antibodies geneknockout migration assays cell activation assays and survival assaysProject 2 What drives CAF development Using similar approachesthis project will address fundamental questions about what drives ahealthy fibroblast to become a CAF and how we can redirect it We aremaking a first-in-class drug to target this process and it needs testingProject 3 The role of fibroblasts in fostering lymph node metastasisFibroblasts switch off anti-tumour T cells in the tumour What effectdoes this have on the ability of T cells to attack tumours in lymphnodes a site of immune activation but paradoxically also an early siteof metastasis This project will use above techniques in human breastcancer cells and mouse models to precisely explore this question
Healthy human colon
Human colorectal Tumor
Epithelium Fibroblasts
18
RESEARCH BACKGROUND
1 NK cell immunosuppressive pathways (with Dr Fernando Guimaraes) Our laboratoryrecently identified the opposing roles of the SMAD and STAT transcription factor families inNK cell anti-tumour activity The intrinsic regulation of these pathways in NK cells and the roleof the tumour microenvironment (TME) to trigger these pathways (via IL-15 IL-12 TGF-β andActivin) will be assessed using transgenic mouse models cell signalling novel therapeuticstrategies and patient samples We aim to identify the molecular basis of NK cell suppressionin the TME to rationally design immunotherapy strategies to overcome them in metastaticcancer
2 Tumour immune evasion (with Dr Jai Rautela) Cancer cells are detected and eradicatedby multiple immune mechanisms including NK cells Cancer cells evolve resistance to intrinsicimmune control and immunotherapy drugs by mutating their genome This project will exploitour unique mouse strains with varying degrees of NK cell function NK cell-dependent tumourmodels validated CRISPR-Cas9 screens bioinformatics and computational biology to dissectthe essential role of NK cells the activating receptor NKp46 and tumour ligands in cancermetastasis NK cell null mice and single cell RNAseq will be used to evaluate the role of NKcells in tumour inflammation including Dendritic Cell and T cell recruitment and activation
3 Integrated NK cell transcriptomics and proteomics (with Dr Fernando Guimaraes) Thisproject aims to elucidate dominant pathways for NK cell anti-tumour immunity usingtranscriptomics proteomics and computation biology Datasets have been generated from NKcell with a large spectrum of tumour surveillance capacities and will be used to undercovernovel and dominant regulatory pathways in NK cells in order to rationalise novel targets forimmunotherapy development Pathways will be confirmed in human NK cells and prioritizedfor next generation chimeric antigen receptor (CAR) NK cells evaluation
HONOURS PROJECTS
Therapies targeting the immune system (immunotherapy) are revolutionising cancer treatment Naturalkiller (NK) cells possess an innate ability to detect and kill cancer cells How NK cells actively detect tumourcells and how cancers evolve to evade immune control is not clear By generating the first specific NK cell-deficient mouse our lab has revealed unique role of NK cells in clearing spontaneous metastases andrecruiting and priming other immune cells in solid tumours Furthermore increasing the activity of NK cellsin vivo by deletion of NK cell checkpoints dramatically reduces tumour burden and with industry partnerswe are developing drugs against these checkpoints for clinical use Cancer remains a major disease burdenas cancer cells can evolve mechanism to evade immune control Using genome-wide CRISPR screenscutting-edge mouse models human genetic variants primary human tumours andproteomicstranscriptomics we have uncovered growth factors and ligands that dictate NK cell ability todetect and kill cancer cells Mechanistic understanding and therapeutic targeting of these pathways is ourresearch goal
NK cell
Dying cancer cell
Cancer Immunotherapy LaboratoryProfessor Nicholas HuntingtonPhone 0467 628 854Email nicholashuntingtonmonashedu httpswwwmonashedudiscovery-institutehuntington-lab
19
Antigen PresentationDr Patricia IllingPhone 03 9902 9373 Email patriciaillingmonasheduhttpsresearchmonasheduenpersonspatricia-illing
RESEARCH BACKGROUNDMy research group integrates proteomics and functional immunology to understand the complexity of antigen presentation by Human Leukocyte Antigen (HLA) class I (HLA-I) molecules This pathway is critical to the activation of CD8+ T cells (cytotoxic T lymphocytes [CTLs]) and shapes the immune response to pathogenic infection and cancer Yet it represents a double-edged sword with the capacity to initiate debilitating autoimmune responses and drug hypersensitivity reactions Understanding the mechanisms of peptide antigen generation and presentation as well as the genetic (HLA-I polymorphisms) cellular (cell type activation state) and environmental factors (viruses therapeutic drugs metabolites) that alter these processes is key to exploitation of this pathway to maximise desirable immune responses (rational vaccine design) and prevent inappropriate immune activation against otherwise healthy tissues Based within the greater Immunoproteomics laboratory (led by Prof Tony Purcell) projects will leverage state of the art mass spectrometry infrastructure therein
HONOURS PROJECTSProject 1 Interference with HLA-I antigen presentation by small moleculesHLA-I present peptides derived from the enzymatic processing of intracellular proteins at the cell surface to generate a summary of cellular protein expression which is surveyed by CD8+ T cells for foreign peptides We have shown that the small molecule drug abacavir can interfere with this process in an HLA allele specific manner causing massive alterations in peptide antigen presentation and unwanted T cell responses which manifest as a drug hypersensitivity reaction (DHR) Numerous other DHRs have been associated with specific HLA alleles and several modes of drug-HLA interaction have been proposed This project aims to develop biochemical and mass spectrometry-based methods to interrogate interactions between small molecules (drugs and metabolites) and both HLA-I molecules and the antigen processing machinery
Project 2 Maximising influenza epitope presentation to inform vaccine designCurrent influenza vaccines generate predominantly antibody based immune responses against the surface glycoproteins of the virus To generate vaccines that also elicit robust T cell responses knowledge of the T cell epitopes involved is required We have used a mass spectrometry-based workflow to define the range of influenza-derived peptides presented by specific HLA-I variants and determine candidate T cell epitopes This project aims to explore the enzymatic processing and presentation of select immunodominant and subdominant T cell epitopes to determine conditions which maximise presentation and immune responses This project will use a mixture of mass spectrometry and cellular assays
Lab head photo
20
B cells Antibody MemoryAssociate Professor Kim JacobsonPhone 03 99029510 Email kimjacobsonmonashedu httpswwwmonashedudiscovery-institutejacobson-lab
RESEARCH BACKGROUNDThe ability of immunological memory to make enhanced responses to subsequent exposures to apathogen underpins immunity The effective utilisation of vaccine-induced humoral memory has left anindelible mark on our potential to live long and healthy lives
Our research studies the ability of the immune system to clear pathogens and form immunity throughproduction of high-affinity neutralising antibody and memory B cells
Very little is known about the factors required for humoral memory Understanding these molecularregulators is core to finding new treatments for B cell-mediated disease amp progressive vaccine design
HONOURS PROJECTS
Project 1 Epigenetic regulation of B cell immune responses
This project will identify new epigenetic regulators of immune memory by investigating histone modifications that allow antibody formation and memory persistence during a secondary response This project can be either a lab-based project or in silico project Lab-based investigating how epigenetic regulators modulate in vivo B cell responses to immunisation or infection In silico using deep-sequencing analysis to investigate the underlying dynamic changes to molecular architecture that occurs during the formation of germinal centres antibody-secreting cells and B cell memory
Project 2 Immune memory dysfunction during chronic infection
Chronic infectious diseases have a devastating effect on global health HIV and Plasmodium falciparum both cause chronic disease and have evaded effective vaccine design SARS-CoV-2 is the newest virus to cause a severe persisting infection with severe disease correlating to dysregulation in humoral responses Production and function of immune memory is altered in chronic infectious diseases leading to rogue memory B cells that may be an impediment to fighting infection This project will investigate the origin and function of these cells and how we can target memory B cells to restore their effectiveness in chronic infection using both in vivo viral models as well as assessment of samples from Covid patients
21
RESEARCH BACKGROUNDOur research examines key cellular processes that are criticallylinked to neurodegenerative diseases and viral infection andimportant targets for novel therapeutic intervention We areinvestigating how the cell responds to proteotoxic stresses andclears potentially cytotoxic protein aggregates in Alzheimersdisease Parkinsonrsquos disease and spinocerebellar ataxia 1 (SCA1)We are also focussed on the host-pathogen interface wherehost-virus interaction is the key to understanding disease andtherapeutic approaches to Dengue (DENV) Zika (ZIKV) andrespiratory tract infections (RSV) for all of which efficaciousvaccines and antiviral agents are lacking
HONS PROJECT 1 NEURODEGENERATIVE DISEASEOur expertise in nuclear trafficking and protein homeostasis (proteasis) provides a unique opportunity toexamine the potential role of specific components of the Hsp70 chaperone network in SCA1 The SCA1disease riving polyQ-Ataxin-1 forms striking nuclear bodies (ATX-NBs) We are documenting thecontribution of specific components of the Hsp70 chaperone network to ATX-NBs with the possibility thatthere could be potential targets to facilitate ATX-NB disaggregation The project will use proximity-basedprotein interaction assays to visualise chaperone localisation with RNA interference (RNAi) and smallmolecule inhibitors against the key chaperones employed to delineate disaggregation potential
HONS PROJECT 2 HOST FACTORS All viruses exploit diverse host cofactors in the infectiouscycle targeting these host proteins offers a way to block viral replication and circumvent the issue ofmicrobial drug resistance Our experience in the host-virus interface and protein chemistry provides aunique opportunity to identify critical novel host co-factors that interact with viral proteins such as thosefrom DENV and RSV This project will characterise newly identified anti-DENV host drug targets utilisingapproaches such as RNA interference (RNAi) coimmunoprecipitation enzymatic assays circulardichroism analytical ultracentrifugation and X-ray crystallography cellular assays and imaging
Nuclear Signalling Proteasis Innate Immunity amp Disease
Professor David A JansDepartment of Biochemistry amp Molecular Biology Tel 99029341 Email davidjansmonashedu httpsresearchmonasheduenpersonsdavid-jans
Dr Nadinath B NillegodaAustralian Regenerative Medicine Institute Tel 99053636 Email nadinathnillegodamonashedu httpsresearchmonasheduenpersonsnadinath-nillegoda
Dr Natalie A BorgRMIT UniversityTel 99253743 Email nataleborgrmiteduau rmiteduaunatalieborg-lab
AsO2
Crystalstructure ofinfluenzadrugRelenza(purple)bound tohPIV3 HA-NA
22
Project 2 Innate immune recognition of viral nucleic acidsBacteria are experts at distinguishing self from non-self This project investigates a family of novel immune sensors that unwind foreign nucleic acids to modify them by ADP-ribosylation Using both nucleic acid biochemistry and cryo-EM students will uncover how this novel immune system selectively marks foreign genetic material an understanding that will reveal how it inhibits viral replication and functions in immunity
Bacteria are embedded in a never-ending struggle with bacteriophages Under pressure bacteria have evolved remarkable defence mechanisms like CRISPR The Knott Lab seeks to uncover the molecular details of how bacterial immune systems specifically sense foreign nucleic acids to protect against infection We aim to better understand the mechanisms of diverse immune systems to enable the development of next-generation tools and CRISPR therapeutics
Nucleic Acid Sensor LaboratoryStructure function and biotechnologyDr Gavin KnottPhone 9905 4399 Email gavinknottmonasheduwwwtheknottlaborg
RESEARCH BACKGROUND
HONOURS PROJECTS
Sensing
Evasion
The pressure of host pathogen interaction drives immune sensor innovation and evasion
Project 3 The molecular basis for precise RNA targetingCas9 is well known as a programmable genome editor because of its ability to precisely cut double-stranded DNA Less well known is the fact that Cas9 can precisely bind and cut RNA an activity that shows great promise as a therapeutic Current projects have the opportunity to drive this therapeutic tool development by uncovering the basis for Cas9 RNA targeting using cryo-EM and RNA biochemistry
Project 1 CRISPR-Cas systems for direct RNA detectionCas13 is a unique CRISPR system that targets viral RNA When Cas13 binds a target RNA it will activate to indiscriminately cut any RNA We have harnessed this behaviour to develop Cas13-based diagnostics for COVID-19 Current projects have the opportunity to use biochemistry andstructural biology to discover how Cas13 enzymes function at themolecular level an understanding that will improve our ability to applythem as diagnostics for Influenza HIV and SARS-CoV-2 viral infection
23
Microbial Oncogenesis LaboratoryDr Terry Kwok-SchueleinPhone 99029216 Email terrykwokmonashedu httpswwwmonashedudiscovery-institutekwok-schuelein-lab
RESEARCH BACKGROUND
PROJECT 1 Understanding how the bacterium Helicobacter pylori stimulates oncogenic signallingvia interaction with the human integrin family of receptorsAim The integrin family of eukaryotic transmembrane receptors play fundamental roles in celladhesion cell migration proliferation angiogenesis and cancer development Activation of MAPkinases and Src kinase are some of the well-characterised signalling events triggered by integrinswhich play key roles in cancer development Interestingly virulence strains of H pylori can potentlyinfluence these signalling pathways In collaboration with other cancer research centres the aim ofthis project is to understand the molecular mechanisms by which the virulence proteins of H pyloriCagA and CagL activate human integrin receptors and how this promotes gastric cancer Techniquesto be used Gene knockdown by RNAi tissue culture transfection live cell imagingimmunofluorescence microscopy Western blotting cloning and animal models
PROJECT 2 How do H pylori virulence proteins activate angiogenesisAim Interesting recent findings indicate that certain amino acid sequence variations of some Hpylori virulence factors are linked to increased gastric cancer risk in infected patients Angiogenesis(the formation of new blood vessels) plays an essential role in tumour development and woundhealing Our preliminary data indicates that certain H pylori virulence factors can activate angiogenicresponses in human endothelial cells cells that make up blood vessels implying that these bacterialfactors may play a key role in tumour development The aims of this project are to characterise thebiochemical properties of these virulent proteins and understand how they contribute to theactivation of angiogenic responses and increased cancer risk Techniques to be used Proteinchemistry molecular cloning protein purification ELISA and angiogenesis assays
HONOURS PROJECTS
Gastric cancer is the 3rd most fatal and 5th most common cancer in humans The molecularpathogenesis of gastric cancer remains poorly understood It is well established that infection byHelicobacter pylori increases the risk of gastric ulcer and gastric cancer Our team uses state-of-the-art molecular biology and cell biology techniques to understand how the virulence proteins of Hpylori lsquohijackrsquo host cell signalling pathways to promote carcinogenesis Our long-term goal is to applythe knowledge gained to the discovery of novel anti-gastric cancer therapeutics and diagnosticmarkers
24
CD8+ T cell activation and functionProfessor Nicole La GrutaPhone 9902 9182 Email nicolelagrutamonasheduhttpswwwmonashedudiscovery-institutela-gruta-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The primary role of CD8+ T lymphocytes (CTLs) is to recognize and remove pathogen-infected cellsand cancers Indeed CTLs play a critical role in mediating protection from infections and cancers inhumans and many strategies exploiting CTL immunity are already in clinical use It is critical thereforeto understand the fundamental mechanisms driving effective T cell activation after antigenencounter The La Gruta laboratory uses a wide range of state-of-the-art molecular and cellulartechniques to elucidate the key drivers of effective T cell immunity and the molecular basis of age-related T cell dysfunction for the elicitation of optimal CTL immune responses
Project 1 Understanding how LckCD8 association influences TCR signalingT cell receptor (TCR) recognition of peptide + MHC class I complexes (pMHCI) is critical for CD8+ Tcell function Despite the extraordinary diversity of the TCR it consistently recognises pMHCI in ahighly conserved orientation We recently showed that this highly reproducible recognition modewas critical for TCR signalling by ensuring that coreceptor-associated Lck (a key kinase essential forinitiating signalling) was colocalized with CD3 allowing for CD3 phosphorylation (Zareie et alScience 2021) Thus coreceptor-associated Lck is critical for constraining how MHC (or MHC-like)
Project 2 Cellular and Molecular Analysis of Ageing in CD8+ T cellsLike many developed countries the population of Australia is ageing with 138 of the populationcurrently over the age of 65 and predictions this will reach 199 by 2031 this increase is predictedto have a considerable effect on the cost to public health services Aged individuals exhibit increasedsusceptibility to and severity of a variety of infections alongside waning vaccine efficacy ratesreflecting in part diminished primary CD8+ T cell responses Studies in mice and humans havedemonstrated that intrinsic defects in CTL immunity contribute substantially to overall immunedysfunction in aged individuals My laboratory aims to elucidate both age related CTL deficienciesand the mechanisms underlying them addressing key aspects including TCR signalling metabolismand epigenetics This work will rigorously define basic immunological epigenetic and metabolicmechanisms restricting intrinsic CD8+ T cell immunity in aged individuals [Co-supervised by DanielThiele Danielthielemonashedu]
We have recently generated mutant mice in which Lck cannotassociate with the CD4 or CD8 coreceptors Using these micewe intend to investigate how coreceptor association with Lckinfluences T cell development TCR repertoire and functionThis work will provide compelling insights into how theadaptive immune system has evolved to optimize T cellspecificity [Co-supervised by Dr Pirooz Zareiepiroozzareiemonashedu]
Conventional Reversedligands are recognized by TCR In particular we show that thecoreceptor by binding Lck can act as a negative regulator ofTCR signalling following unconventional TCR-pMHC recognition
25
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Dendritic Cell Receptors Associate Professor Mireille LahoudPhone 9905 3788Email mireillelahoudmonashedu httpswwwmonashedudiscovery-institutelahoud-lab
RESEARCH BACKGROUNDOur research focus is understanding how the sentinels of the immune system the dendritic cells (DC) sense and respond to ldquodangerrdquo in their environment and to use this knowledge for improving vaccines and immunotherapies DC have an array of receptors designed to detect pathogen-associated and damage-associated molecular patterns These receptors enable DC to sense invading pathogens or other danger (eg damaged or dead cells) and to direct the type of protective immune response required Importantly there are multiple DC subsets which are tailored for different functions DC subsets can recognise different pathogens and damage signals and respond accordingly Our focus is to determine the receptors that enable the DC to sense and respond to such signals and their role in inducing immune responses
RESEARCH PROJECTSProject 1 Dendritic cell receptors dead cell recognition and immune modulationDC monitor the environment for potential ldquodanger signalsrdquo that signify pathogen invasion including non-homeostatic cell death caused by viruses As an example we identified a DC-specific receptor Clec9A which plays an important role in the recognition and processing of antigens (Ag) acquired from such dead cells to initiate effective immune responses Furthermore Clec9A is a particularly effective target for the delivery of Ag directly to DC subsets for immune modulation
This project will elucidate the molecular interactions of key dendritic cell receptors and determine the role of these interactions in regulating DC biology and the modulation of immune responses
Project 2 Molecular Mechanisms that underpin dendritic cell cross-presentation DC take up process and present antigen (Ag) to T cells to initiate immune responses There are multiple DC subsets that are tailored for different functions While all DC can take up process and present Ag on MHC II to induce CD4 T cell responses only particular DC subsets can take up dead cells and other exogenous Ag and cross-present these on MHC I to induce the CD8 T cell responses essential for killing infected cells and tumours We have identified a panel of genes that are selectively expressed by cross-presenting DC subsets In this project we aim to investigate the expression and function of these genes and determine their role in Ag presentation and DC function
26
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Fibrinolysis and Wound HealingDr Ruby LawPhone +61 3 99039308 Email rubylawmonasheduhttpswwwmonashedudiscovery-institutelaw-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Plasmin plays a vital role in fibrinolysis tissue remodeling wound healing and cell migration Duringtraumatic injuries and systemic pathogen infections inhibition of plasmin and fibrinolysis save lives Onthe other hand in the case of ischemic stroke and pulmonary embolism therapeutically promotingplasmin formation promotes blood clot dissolution and blood flow Our studies investigate theintermolecular structure and function relationships of the plasminogen activation system
Key research techniques X-ray crystallography cryo-electron microscopy enzyme kinetics flowcytometry small angle x-ray scattering surface plasmon resonance mass spectrometry and novelmonoclonal antibody discovery
1 Characterization of plasminogen and receptor interactions in macrophage function (with DrEleanor Leung)
2 Targeting plasmin activity in infections and inflammations (with Dr Jason Wu)
3 Improving the outcome of tissue transplantation therapy (with Prof Whisstock)
The group A streptococcal plasminogen-binding M protein and plasminogen kringles( DOI 101016jjmb201907003)
Inhibition of Clostridium difficile infection by anti-plasmin monoclonal antibody (DOI 101053jgastro202006032)
27
Mitophagy amp mitochondrial quality control in diseaseDr Michael LazarouEmail michaellazaroumonasheduhttpswwwmonashedudiscovery-institutelazarou-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
microscopy the latest generation ofgenome engineering technology(CRISPRCas9) tissue culture westernblotting stable protein expression usingretrovirus molecular biology and massspectrometry These techniques enablestudents to gain experience in a range ofscientific approaches and providestudents with a strong scientificfoundation to build on
Project 1 Characterisation of novel PINK1Parkin mitophagy factors Using quantitative proteomicsof autophagy defective cell lines we have identified a number of novel PINK1Parkin mitophagy candidateproteins Some of these proteins have predicted functions in vesicle trafficking and membrane fusion whileothers have no known function This project will utilise CRISPRCas9 gene editing to generate knockout celllines of the putative novel mitophagy factors in order to determine whether the factors are required forPINK1Parkin mitophagy Furthermore how the factors regulate the molecular signals that govern theclearance of defective mitochondria will be investigated For example are they required for autophagosomeformation or for the recognition of damaged mitochondria
Project 2 Can bacterial infections predispose you to Parkinsonrsquos Disease There is a growing bodyof evidence linking inflammation to neurodegeneration in Parkinson Disease Some of the latest research inthe field has revealed that PINK1Parkin mitophagy plays a key role in preventing inflammation (Sliter etal (2018) Nature) PINK1 and Parkin clear damaged mitochondria before they rupture and release theirmitochondrial DNA which is the source of inflammation This project will investigate whether pathogenicbacteria which damage mitochondria can cause excessive inflammation when mitophagy is defective Bonederived macrophages from WT and Parkin KO mice will be infected with different bacteria (eg Salmonellaor Legionella) to assess whether Parkin can play a protective role in mitigating mtDNA derivedinflammation during infection The role of other mitochondrial quality control systems will also beinvestigated with the aim to find new pathways that we can target to help prevent Parkinsonrsquos Disease
3D reconstruction of a mitochondrion (red) within an autophagosome(green) during PINK1Parkin mitophagy using advanced light andelectron microscopy
Parkinsonrsquos disease (PD) is one of the most common of the neurodegenerative disorders affecting 1-2 of thepopulation worldwide Multiple lines of evidence place mitochondrial dysfunction as a central player in thepathogenesis of PD Two proteins commonly mutated in familial PD PINK1 and Parkin play a key role inmaintaining mitochondrial health by identifying damaged mitochondria and degrading them through aselective form of autophagy termed mitophagy (Lazarou et al (2015) Nature) Our lab investigates themolecular mechanisms of PINK1Parkin mitophagy We are interested in how PINK1 and Parkin drive thesequestration of damaged mitochondria within double membrane structures called autophagosomes beforedelivering them to lysosomes for degradation The PINK1Parkin mitophagy projects on offer provideexperience with a variety of biochemical and cell biological techniques including state-of-the-art confocalt
28
Comparative ImmunologyDr Jeacuterocircme Le NoursPhone 99050751Email jeromelenoursmonasheduhttpswwwmonashedudiscovery-institutele-nours-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
While most studies in adaptive immunity have focused on peptide-mediated immunity my research aims to explorethe unchartered territory of lipid- and metabolite-mediated immunity This aspect of immunity represents a newfrontier in immunity Indeed there is a number of pressing fundamental questions that need to be addressed (i)What is the extent of the chemical diversity of immunogenic non-peptidic antigens (Ags) Are there more atypical Agsto be discovered in mammalian and non-mammalian species (ii) How are these lipid and metabolite Ags presentedand recognized (iii) What are the molecular mechanisms that underpin the recognition event and the signallingoutcomes (iv) How did non-classical MHC molecules evolve to fulfill their molecular functions within a specificspecies By applying a multi-disciplinary and highly innovative approaches that include comparative immunologychemistry structural biology cell immunology advanced atomic and molecular imaging my research program aimsto provide comprehensive and fundamental insights into molecular recognition of non-peptidic Ags and gain anevolutionary perspective on the structure and function of MHC-like Ag-presenting molecules
1 To explore the field of comparative immunology (Structure and function of non-classical MHC molecules (MHC-like) in evolutionary distinct species eg Marsupials frogs chickens and bats)
In the past decade the development of technologies has opened new exciting frontiers and novel opportunities toexplore the diversity of immunity in mammalian and non-mammalian species There is indeed tremendous value andexcitement to discover how the immune system in different organisms (non-human non-mouse) work and moreimportantly to understand how distant species adapted to their immediate environment in order to survive exposureto pathogens throughout evolution Addressing these fundamental questions may have significant impact in relationto the origin and function of the immune system These projects aim to investigate the biological function of MHC-like molecules in evolutionary distinct species to humans and will be focusing on the functional and structural studiesof families of MHC-like from a wide range of vertebrate species spanning more than 360 millions years of evolutionincluding frogs marsupials guinea pigs Tasmanian devils bats and rabbits These projects will involve a number ofbiochemistry- and biophysical-based techniques including the recombinant expression purification crystallizationand 3D structure determination of immune molecules using X-ray crystallography
2 To Determine the structurefunction relationship for human NKT TCRs that interact with tumour-derived lipidAgs
This project will explore the human NKT TCR molecular recognition of human tumour-Ags that are associated withvarious types of human cancer and their resemblance to α-GalCer the prototype NKT cell agonist suggests that theymay be targeted by NKT cells Gangliosides include the disialoganglioside GD3 a tumour-associated Ag that isimmunostimulatory for a subset of mouse NKT cells We have identified subsets of NKT cells that respond to the self-tumour Ags GD3 and and α-FucCer Furthermore through our international collaborations we have access to arange of synthetic analogues of α-FucCer that will enable us to explore human NKT cell recognition of this family ofAgs This project will aim to determine the structure of the NKT TCRs in complex with their CD1d-restricted tumour-associated ligands that will permit to establish fully the specificity determinants of these NKT TCR-mediatedinteractions with tumour-associated Ags This project will involve the use of a wide range of methods that includebiochemical and biophysical techniques (Protein expression and purification surface plasmon resonance (SPR) and X-ray crystallography) 29
Clinical Immunology GroupDr Nicole MifsudPhone 03 9902 9311 Email nicolemifsudmonasheduhttpswwwmonashedudiscovery-institutemifsud-lab
RESEARCH BACKGROUNDMy group examines key interactions between T cells and human leukocyteantigen (HLA) molecules that are not only imperative for control and clearanceof pathogens such as viruses but also are pertinent to many human disorders(ie autoimmunity allergy cancer) and therapies for end-stage disease (ietransplantation) In particular my interests explore how the antigen-specific Tcell repertoire shaped by previous exposure to environmental pathogens isable to influence future immune responses through T cell receptor (TCR) cross-reactivity This TCR cross-reactivity can in certain scenarios generate adverseimmune responses that affect target organs in the setting of transplantationand may contribute to the onset of autoimmunity
HONOURS PROJECTSProject 1 Targeting antigen-specific T cells in transplantationTransplantation of organs tissues or cells is a successful treatment for organ failure traumatic injuries andblood cancers In most cases genetic differences exist between the donor and recipient and immuneresponses to foreign transplantation antigens cause graft rejection and graft versus host disease (GvHD)Current standard of care involves global inhibition of these responses either using immunosuppressivedrugs or by depletion of immune cells from donor stem cells However these approaches do notdistinguish between harmful immune responses directed against the transplant or the recipientrsquos normalcells and protective immune responses against pathogens or cancer T cells which can recognise foreigntransplantation antigens presented by human leukocyte antigen (HLA) molecules are termed alloreactiveand can mediate destructive immune responses that compromise graft function and survival This projectwill characterise alloreactive CD8+ T cells across different HLA mismatches and explore their recognition ofimmunogenic peptideHLA complexes thereby contributing to alloreactivity Experimental techniques willinclude basic bioinformatics cellular assays flow cytometry RT-PCR and DNA sequencing
Project 2 Virus-specific T cells may drive drug hypersensitivity reactions via T cell cross-reactivityAdverse cutaneous drug reactions are often common immune-mediated responses associated with severeillness and in some instances high rates of mortality Yet our understanding of how sensitization occursand the underlying immunologic mechanisms inducing the immune response remains unclear Oneproposed theory is that of heterologous immunity whereby virus-specific T cells cross-react againstthe drug-altered peptide repertoire presented on autologous HLA molecules We have preliminaryevidence that a human HIV Gag TW10HLA-B57ndashspecific T cell clone recognises autologous HLA-B57 butonly in the presence of the antiretroviral drug abacavir This suggest that HIV-specific memory T cells canthemselves participate in abacavir-induced hypersensitivity reactions through T cell cross-reactivity Thisproject will explore the drug-altered peptide repertoire presented by skin and liver derived cell lines(target tissues of the drug reaction) that activates the HIV Gag TW10HLA-B57ndashspecific T cell cloneExperimental techniques will include cellular immunology flow cytometry immunoaffinity purificationsHPLC and mass spectrometry This project is co-supervised by Prof Anthony Purcell
Lab hedphoto
30
Mitchell LabProfessor Christina Mitchell
Email christinamitchellmonashedu
Web page httpsresearchmonasheduenpersonschristina-mitchell
RESEARCH BACKGROUNDCells respond to changes in their microenvironment by activation of complex signalling cascades The phosphoinositide 3-kinase (PI3K) signalling pathway is involved in a number of cellular processes such as cell growth survival migration and differentiation PI3K is a proto-oncogene in up to 30 of all human cancers Additionally deregulation of the PI3K pathway occurs in many other human diseases including diabetes and muscular dystrophy as well as in developmental disorders
Our laboratory focuses on a family of PI3K regulatory enzymes that are critical regulators of the PI3K pathway and regulate many cellular functions Mutation or altered expression of inositol polyphosphate phosphatases has been detected in human diseases such as Marinesco-Sjogren Joubert and Lowe syndromes breast cancer insulin resistance leukaemia and degenerative neuropathies
HONOURS PROJECTSRole of PI3K regulatory enzymes in development and cancerContact ChristinaMitchellmonashedu LisaOomsmonashedu MicheleDaviesmonasheduRegulation of PI3K signalling is crucial for embryonic development and physiological homeostasis PI3K signalling is deregulated in developmental disorders and in many human diseases including cancer diabetes and retinopathies We have shown that loss or inactivation of PI3K regulatory enzymes leads to defects in embryonic development We have also shown that loss of these enzymes affects tumour initiation progression and metastasis in mouse cancer models Recent clinical trials using PI3K inhibitors have indicated the potential of these drugs for targeted anti-cancer therapy therefore identifying cancers with amplified PI3K signalling is of critical importance for optimising treatment strategies These projects will utilise animal models and genetic manipulation in cell culture to investigate the role of PI3K regulatory enzymes in development and cancer Overall these projects aim to identify and characterise novel therapeutic candidates for PI3K-driven disease and development disorders
Skeletal muscle disease identification of causes and novel therapiesContact ChristinaMitchellmonashedu MeaganMcGrathmonasheduSkeletal muscle homeostasis is essential for human health and mobility The human muscular dystrophies and myopathies describe a broad range of debilitating human muscle diseases with affected individuals often suffering significant muscle weakness loss of mobility and in severe cases early mortality This project will utilise transgenic knockin and knockout mouse models to identify and characterise the molecular mechanisms of human muscle disease with particular emphasis on fundamental muscle processes including autophagy regenerationrepair metabolism and muscle stem cell function This research aims to understand the causes of human muscle disease to uncover potential treatment strategies for sufferers
31
Macrophage-Pathogen Interaction LabDr Thomas NadererPhone 9902 9517Email thomasnaderermonasheduwwwmonashedudiscovery-institutenaderer-lab
RESEARCH BACKGROUNDSuperbugs are not only resistant to current antibiotics but they are also highly effective in evadingimmunity This leads to several human diseases that are increasingly difficult to treat Thus there is anurgent need to develop alternative approaches to antibiotic therapy Rather than killing the bacteriatargeting host-factors that promote pathogen survival has emerged as a promising strategy ininfectious diseases To develop this further we need a better understanding about how superbugsevade immunity on the molecular and cellular levels
To identify new host-pathogen interactions we follow infections by live-cell imaging This enables theidentification of host cell responses on the single cell level in a high-temporal resolution In additionwe employ super-resolution imaging to uncover how pathogens target host factors in immune cellsFinally by screening host genome libraries we identify the host factors that enable superbugs tosurvive immune attack This has led to new therapeutic approaches by re-purposing existing drugs tokill infected cells (Speir et al Nature Micro 2016)
HONOURS PROJECTS1 Targeting host factors to prevent MRSA infections
Methicillin resistant S aureus (MRSA) utilizes secreted toxins to kill innate immune cells and tocause disease The project will identify host factors that are activated by these toxins For thisa whole genome CRISPR library will be screened to identify mutant immune cells that resisttoxin mediated killing Identified genes will be further validated in infections that depend ontransgenic stem-cell derived human immune cells This will utilize live-cell imagingimmunological and biochemical assays
2 Cell death signalling in infectionsThe superbug Neisseria gonorrhoeae that causes sexually transmitted infections evadesimmunity but the mechanism behind this remain unclear We have identified bacterialsecreted vesicles as novel delivery system employed by these bugs to manipulate cell deathsignalling to evade immunity The project will utilize proteomics and transcriptomics tocharacterize bacterial vesicles In addition super-resolution imaging will identify how vesiclesdeliver bacterial proteins into immune cells to hijack host signalling pathways This will identifyhost-pathogen interactions that promote infectious diseases
32
Integrated Network Modelling LaboratoryDr Lan NguyenPhone 990 51298Email LanKNguyenmonasheduwwwmonashedudiscovery-institutenguyen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Nguyen Lab develops and exploits highly interdisciplinarysystems biology approaches that integrates experimental lab-based experiments with computational modelling bioinformaticsand machine learning to address fundamental biological andbiomedical challenges with a focus on cancer research
Students will benefit from a strong interdisciplinary and highlystimulating research environment through regular interactionwith researchers having both lsquodryrsquo and lsquowetrsquo expertise enablingthem to develop unique mixed skillsets Depending on thebackground and interest the students can undertake researchprojects that are primarily lab based or computational orcontaining mixed wetdry components Current projects aredescribed below However interested students are encouragedto contact Dr Nguyen to discuss specific projects
Project 1 Elucidating adaptive resistance to anti-cancer targeted therapy The arrival of targeted therapies hasrevolutionized cancer treatment yet drug resistance remains a major clinical challenge Like ants who are acuteat seeking alternative routes when their path is blocked cancer cells manage to find escape paths to bypassdrug treatment by rewiring their signalling networks but how exactly they do that is poorly understood Thisproject aims to elucidate these escape paths and identify ways to block them by combining multiple drugswhich will lead to new treatment strategies It employs a range of state-of-the-art biochemical and cellularassays to investigate the question The data generated by the student can be used to construct computermodels (by modellers in the lab) that describe drug response processes and further guide experimentsProject 2 Optimising drug scheduling for combination therapies against cancer Frequent resistance to single-agent treatment means that doctors are turning to combination therapy ie lsquococktails of drugsrsquo to beatresistance We found that the exact timing and order that drugs are combined can have a huge effect on theirability to kill cancer cells This project aims to explore various scheduling strategies for drug combinations withthe goal to maximize treatment benefit by enhancing efficacy while reducing toxicityProject 3 Exploiting the PI3K-Akt-mTOR network for cancer therapies The PI3K-Akt-mTOR signalling pathwayis one of the most frequently dysregulated pathways across many different solid cancer making it a promisingtherapeutic target However it interplays with many other pathways and the complexity makes it hard topredict how to effectively target this pathway in conjunction with other pathways This project will employ anintegrative systems approach to gain network-level understanding of PI3K signalling A current focus is onelucidating the role of DEPTOR a key node in the pathway and how to exploit this protein for cancer therapyProject 4 BioinformaticsMachine Learning approaches to predict biomarkers for cancer therapy This projectaims to employ data science methods including bioinformatics and machine learning approaches to integrateand analyse various types of molecular and drug response data in order to discover predictive biomarkers thatcan inform which patients will benefit (or not) from a particular targeted treatment A preliminary frameworkhas already established in the lab and the project will build upon this foundation This project is ideal forsomeone with skills and interest in data science bioinformatics or machine learning Knowledge in R andorPython Matlab is desirable but not mandatory
33
Dendritic Cells in Health amp Disease Associate Professor Meredith OrsquoKeeffe Phone 9905 3549 Email meredithokeeffemonashedu httpswwwmonashedudiscovery-instituteokeeffe-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Dendritic cells are sentinels of the immune system that produce cytokines and interferons upon sensingdanger They are also professional antigen presenting cells thereby connecting the innate and adaptiveimmune systemsOur laboratory investigates how pathogens and their products or danger signals of lsquoselfrsquo activate dendriticcells We aim to decipher how this activation influences the function of dendritic cells We aim to understandthe role of dendritic cells in interferon-mediated diseases including autoimmune diseases such as Lupus incancer immunotherapies and in antibiotic-resistant bacterial infections
1 The function of checkpoint inhibitors on dendritic cellsThe anti-tumour effects of immunotherapies targeting checkpoint inhibitors is currently attributed to thelsquore-awakeningrsquo of T cells However we have now discovered that DC can express high surface levels ofcheckpoint inhibitors We find that the functions of dendritic cells are themselves directly regulated bycheckpoint inhibitor expression This project will examine the biological consequences of and molecularpathways leading to checkpoint inhibitor regulation of dendritic cell function
2 The effects of interferon-lambda on dendritic cellsInterferon-lambda is an anti-viral cytokine that is highly expressed by dendritic cells and attributed withmajor regulatory roles in the immune system This project will investigate the effects of interferon-lambdaon dendritic cell function It will particularly examine the nature of the interferon-lambda receptor ondendritic cells
34
Cancer Biology laboratoryDr Antonella PapaPhone 9902 9330Email antonellapapamonasheduhttpswwwmonashedudiscovery-institutepapa-lab
HONOURS PROJECTS
RESEARCH BACKGROUNDCancer is a complex disease that evolves over time and becomes progressively more malignant byacquiring multiple genetic alterations The PI3K-Akt-mTOR cascade is a key intracellular signallingpathway that mediates several biological processes including cell growth proliferation and metabolismPTEN (phosphatase and tensin homologue deleted on chromosome 10) is a major tumour suppressorthat inhibits PI3K pathway activation and is frequently mutated in a range of human cancer and cancersyndromesThrough a combination of in vitro studiesand in vivo analyses we use novel mousemodels of human cancers to investigatehow loss of PTEN functions alters normalcell behavior to promote cell survival andcancer progression with a special focus onbreast cancerMoreover we aim to characterise the mechanisms of action of PTEN and to define its role insuppression of tumourigenesis beyond its functional interaction with the PI3K pathwayThe final goal of our studies is to ultimately identify new therapeutic targets regulated by PTEN andpropose novel treatment modalities of human diseases associated with PTEN mutations
1 Validation of candidate Pten-targets We have performedphosphoproteomics of primary cells derived from two knock-in mouselines harbouring loss-of-function and cancer-associated mutations inPten These mutations differentially affect the lipid or the lipid andprotein Pten phosphatase activities and as a result their expressioninduces activation of distinct signalling pathways This project aims tovalidate the activation status of newly identified Pten-regulatedpathways and entails the execution of a number of experimentsincluding i) expansion treatment and purification of human andmouse cell lines ii) protein analyses and iii) gene expression profiling2 Mammary gland morphology and tumour onset of mutant miceWe have generated new mouse models expressing mutant version ofPten in combination with additional oncogenic mutations and this hasresulted in rapid mammary tumour formation To characterise tumouronset and assess how alterations in the mammary gland developmentcontributed to this phenotype we plan to collect fat pads fromexperimental and control mice and study branching morphogenesisand evolution of epithelial buds over time This projects requiresworking with animal models processing of mouse tissues and anumber of immunostaining techniques
carmine alum-stained wholemountof 12 weeks old mammary gland
35
We recommend a small picture here - your photo
or backgrounddata image
Immunoproteomics LaboratoryProfessor Anthony PurcellPh 99029265 Email anthonypurcellmonashedu httpsresearchmonasheduenpersonsanthony-purcell httpswwwmonashedudiscovery-institutepurcell-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
The Purcell laboratory specialises in identifying new targets of the immune response using a combination of functional immune profiling proteomics metabolomics transcriptomics and structural biology The laboratory has an outstanding track record in delivering highly impactful studies in antigen discovery and the fundamentals of antigen processing and presentation including recent publications in highly regard journals including Science Nature Nat Immunol Sci Immunol PNAS J Exp Med Immunity J Clin Invest Cancer Immunol ResThe Purcell lab works closely with other groups at Monash nationally and internationally to study all aspects of immune recognition We work closely with industry and pharma to translate our findings into the clinic with major collaborations with local European (Belgium Denmark UK) and US based pharma and startups
Novel peptide antigens in infectious disease autoimmunity and cancerProject Description Recent studies have highlighted a prominent role for a novel classes of peptides generated by cancer specific mutations alternative reading frames and intronic regions and various post-translational modifications including proteasomal splicing of different polypeptide chains (1-2) Along with their more conventional counterparts these peptides represent an untapped resource for vaccination and immunotherapy Our lab has developed new tools to identify and study these peptides (3-9) Several projects of relevance to influenza infection psoriasis rheumatoid arthritis diabetes melanoma lung brain and bowel cancer are available The projects will involve biochemistry mass spectrometry andor immunology focussed techniques Our lab has access to cutting edge instrumentation collaborates through a world wide network of scientists and industry to deliver research and health outcomes including the inclusion of our novel peptide antigens in clinical trialsReferences1 J Liepe et al A large fraction of HLA class I ligands are proteasome-generated spliced peptides Science 354 354-8 (2016)2 A Purcell S Ramarathinam N Ternette Mass spectrometry-based identification of MHC-bound peptides forimmunopeptidomics Nat Protocols 14 1687-1707 (2019)3 P Faridi et al Spliced peptides and cytokine driven plasticity govern the immunopeptidome of melanoma CancerImmunology Research 8 1322-34 (2020)4 M Koutsakos et al Human CD8(+) T cell cross-reactivity across influenza A B and C viruses Nat Immunol 20 613-25(2019)5 K Pandey et al In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementarypeptide enrichment and mass spectrometric acquisition strategies Mol Immunol 123 7-17 (2020)6 S Mei et al Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly fromdeglycosylated precursors Mol Cell Proteomics 19 1236-47 (2020)7 N Croft et al Most viral peptides displayed by class I MHC on infected cells are immunogenic PNAS 116 3112-17 (2019)8 P Faridi et al A subset of HLA-I peptides are not genomically templated Evidence for cis- and trans-spliced peptideligands Sci Immunol 3 eaar3947 (2018)9 T Wu et al Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTLresponses Nat Commun 10 2846 (2019)10 G Goncalves et al IFNγ modulates the immunopeptidome of triple negative breast cancer cells by enhancing anddiversifying antigen processing and presentation Frontiers Immunol 12 645770 (2021) 36
Advanced Cellular Imaging Lab AProf Georg Ramm Phone 9905 1280Email georgrammmonashedu wwwmonashedudiscovery-instituteramm-lab wwwmonasheduresearchinfrastructurecryo-em
Background Our lab is focused on high-resolution imaging of cellular architecture and intracellular trafficking We are the first in Australia to use cryo-tomography (on Titan Krios) in combination with cryo-focused ion beam milling (cryo-FIB on cryo-Helios) to reveal cellular structures at the highest resolution We focus on fundamental cell biological problems that are relevant to human diseases This includes the intracellular degradation of organelles by autophagy and mitophagy mitochondrial ultrastructure and dynamics in healthy and stressed cells and cellular structural changes during cell death
HonoursPhD Project 1 High-resolution imaging of mitochondria under stress Cryo-electron tomography (CET) allows for the highest resolution cellular imaging achievable at the moment To get access to all areas of the cell we use CET in combination with cryo-focused ion beam milling to cut windows into thicker parts of the cell In collaboration with the Kile lab we were the first to show herniation of the inner mitochondrial membrane (green) through an apoptotic pore in the outer membrane (red) in apoptotic cells We will use high resolution imaging to investigate how macromolecules such as ATP synthases (yellow) in the crystae membrane (blue) are undergoing changes during apoptosis
HonoursPhD Project 2 Correlative light and electron microscopy of autophagy Our lab is applying and developing new imaging tools such as cryo-correlative light and electron microscopy to combine state of the art optical and electron microscopy techniques The project will apply these high-resolution techniques to study the spatio-temporal regulation of intracellular organelle traffic in autophagy
HonoursPhD Project 3 Molecular Imaging of key metabolic signalling nodes We use cryo-EM to determine molecular structures of key molecules involved in the metabolic regulation of cells While structural cryo-EM is traditionally being used to solve molecules larger than 100kDa we will apply recent advances that allow for high resolution imaging of smaller molecules
37
and consequently autoimmunity Indeed in addition to the role of HLA in protective immunity they arealso important genetic determinants in autoimmunity We are interested in how post-translationalmodifications such as citrullination deamidation and hybrid peptide generation leads to the conversion ofself and innocuous environmental derived peptides (eg gluten peptides in celiac disease) into antigenictriggers for a deleterious immune response We investigate how these neo-antigens are presented by MHCClass II (MHC-II) molecules and how these complexes are recognised by the T cell receptor (TCR) on CD4+ Tcells that initiate these disease processes Other projects being pursued involve understanding differencesbetween T cell antigen recognition by regulatory and effector T cells in autoimmune disease The projectsdescribed below will employ biochemical biophysical structural and cell based approaches to investigatethe cellular immune response to self and modified self antigens in autoimmune and inflammatory diseases
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Structural Autoimmunity Dr Hugh ReidPhone 9902 9237Email HughReidmonashedu httpsrossjohnlabcomlaboratory-groupresearch-team-hugh
Human Leukocyte Antigens (HLA) molecules of the majorhistocompatibility complex (MHC) regulate the adaptive immuneresponse HLA molecules present peptides derived from self andnon-self proteins to T cells as a means to detect and destroyinvading pathogens The capacity to distinguish between peptidesderived from self and non-self proteins is thus a crucial feature ofthe immune system However failure of this selfnon-selfdiscrimination can result in T cell reactivity against self-peptides
Project 1 The basis for T cell cross-reactivity between gluten antigens in coeliac diseaseIn coeliac disease (CD) the T cell response to gliadin peptides derived from gluten in wheat barley and ryehas been well characterised Whilst some gluten peptide antigens generate a T cell response that is highlyrestricted to that antigen other gluten antigens can elicit a response whereby the same T cell can recognisemore than one antigen This project will characterise how TCRs isolated from such cross-reactive T cells canrecognise multiple peptides sequences presented by HLA-DQ2 the major disease predisposing allele for CDProject 2 The role of neoantigen generation in the pathogenesis of type 1 diabetesA newly discovered mechanism for the generation of antigenic peptides in type 1 diabetes (T1D) involves thesplicing of insulin with other pancreatic peptides to form hybrid insulin peptides (HIPs) A CD4+ T cellresponse to these peptides has been demonstrated in T cell clones isolated from T1D patients This projectaims to understand the structural basis for the presentation of such HIPS in HLA allomorphs associated withT1D as well as how the TCRs of responsive T cells recognises the HIP peptides bound to HLA Furthermorewe wish to determine the phenotype and TCR gene usage of the responding repertoire of CD4+ T cells tounderstand how HIPS shape the immune response in T1DProject 3 Defining key determinants of HLA mediated T cell tolerance and autoimmunitySome HLA alleles predispose individuals to autoimmunity whereas others provide dominant protectionagainst disease We have have provided a mechanism for dominant protection by demonstrating inGoodpasturersquos Disease (GP) a kidney autoimmune disease that HLA molecules encoded by the susceptibilityand protective alleles both present the dominant autoantigenic peptide but stimulate Teff (disease causing)and Treg (protective) cells respectively This project will determine the phenotype and function of GPpeptide specific Treg cells how different HLA presentations of the same peptide affect T cell repertoire andphenotype and to define how peptide-HLATCR interactions determine phenotype and function
38
Nutrient Metabolism amp Signalling LabDr Adam J RosePhone 9902 9340 Email adamrosemonashedu
httpswwwmonashedudiscovery-instituterose-lab
RESEARCH BACKGROUNDThe tight regulation of metabolic control is important for organismalfunction and wellbeing We investigate the pathways by which ingestednutrients coordinate proper function and particularly how certainnutrient signalling pathways talk to each other when nutrient balance isaltered such as in obesity diabetes liver disease and cancerProjects
Liver-muscle crosstalk in wasting diseases We have recently published(Okun et al Nature Metabolism 2021) that liver-muscle metabolic crosstalk isimportant for metabolic disease This project will further investigate this linkin wasting diseases such as severe diabetes liver disease and cancer
Novel liver signalling nodes in metabolic control Glucagon is an importanthormone in metabolic control but the signalling pathway by which it exerts itsmany effects is essentially a lsquoblack boxrsquo Capitalising on our novel lsquoomics dataand established molecular tools we are currently investigating newsignalling hubs engaged by glucagon to uncover new facets of the biology ofthis pivotal hormone
Novel stress signalling pathways to prevent age-related metabolic declineWhile prolonged severe stress is bad mild and intermittent stress appears tobe pro-adaptive and protects from age related metabolic decline andpathologies We have uncovered that mitochondrial stress signalling is acommon feature of improved health and longevity with dietary restrictionstrategies This project will investigate the signalling pathways andhormones necessary to convey these benefits in order to find ways tomimic these benefits
Techniques pre-clinical mouse models standard and viral genetic gainloss-of-function ex vivo organ culture cell culture in vivo and ex vivo metabolic tracingmetabolite assays phospho-proteomics metabolomics histology molecularbiology (cloning western blot ELISA etc)
39
Cancer functional Genomics labAProf Joseph (Sefi) RosenbluhPhone 99029257 Email sefirosenbluhmonashedu Webpage httpswwwrosenbluh-labcom
RESEARCH PROJECT BACKGROUNDOur limited ability to systematically study the function of genes and how they arederegulated in cancer has limited our ability to treat and understand cancer To address thisbottleneck we have been at the forefront of functional genomics and have developed anarray of tools mostly based on CRISPR technology that enable high throughput cost efficientstudies of genes and how they function in normal cells or during disease progressionProjects in the lab use unbiased CRISPR based genetic screens to identify drug targets incancers with defined genomic alterations Our ultimate goal is to develop cancer therapiesthat will be tailored to specific patients based on defined genomic features
2020 HONOURSPhD PROJECTS1 Identification of genes that induce breast cancer risk Breast cancer is a leading cause ofdeath in women At least 35 of breast cancer cases are due to genetic familial mutationshowever we currently understand only a small number of these mutations Identifying thesemutations is particularly significant since these could be used for development of drugs thatreduce breast cancer risk or could treat patients with breast cancer This project will use stateof the art CRISPR based technologies aimed at identifying the genes that induce breastcancer risk
2 The role of circular RNA in cancer Since the discovery of RNA 150 years ago we havegained good understanding of mRNA and only recently have we begun to uncover the roles ofother RNA types One such RNA that has been previously overlooked since it is difficult todetect using conventional sequencing strategies is circular RNA (circRNA) CircRNAs are highlyabundant and initial studies have demonstrated important functions for some circRNAs Yetfunctional studies of circRNAs are limited due to the absence of tools to systematicallyperturb circRNAs without affecting the function of the linear RNA This project will use ourcurrently developed CRISPR based approaches to inhibit circRNAs and identify circRNAs thatare important for cancer progression
3 Development of new therapeutic molecules PROTACs are new and exciting type ofinhibitors that work by by recruiting a ubiquitin ligase and degrading a protein of interestThis project will develop new approaches to identify PROTACs that inhibit cancer growth andcould be used for cancer treatment
40
RESEARCH BACKGROUND
Immune Recognition LaboratoryProfessor Jamie Rossjohn FAA FLSW FAHMS FMedSciARC Australian Laureate FellowEmail JamieRossjohnmonasheduLab webpage httpsrossjohnlabcom
HONOURS PROJECTS
The academic research program within this laboratory is focused on defining thekey molecular interactions underlying receptor recognition events that are theprimary determinants of cellular immunityThe laboratoryrsquos research has provided an understanding of the basis of peptidemetabolite and lipid presentation ndash events that underpin protective immunity anddeleterious immune reactivity The teamrsquos research on anti-viral immunity hasprovided an understanding of the factors that shape MHC-restriction (eg NatureImmunology 2015 Immunity 2016 Science 2021) while also demonstrating howthe pre-TCR a receptor crucial for T-cell development functions by autonomousdimerization (Nature 2010) In relation to aberrant T-cell reactivity our team hasprovided insight into alloreactivity (Immunity 2009) HLA and autoimmunity(Nature 2017) Celiac Disease (Immunity 2012 NSMB 2014 amp 2019 Cell 2019)rheumatoid arthritis (JEM 2013 amp Science Immunol 2021) and HLA-linked drughypersensitivities (Nature 2012) Regarding innate and innate-like recognitionthe team has shed light into how Natural Killer cell receptors interact with theircognate ligands and viral immunoevasins (Nature 2011 JEM 2016 NSMB 2017Cell 2017 PNAS 2018) Further we have provided fundamental insight into TCRrecognition of lipid-based antigens in protective and aberrant immunity (egNature 2007 Nature Immunology 2016 Nature Immunology 2018 amp 2020) Mostrecently our team identified the long sought after ligand for MAIT cells namelyshowing that MAIT cells are activated by metabolites of vitamin B and can alsorespond to commonly prescribed therapeutics (Nature 2012 2014 NatureImmunology 2016 2017 2020 Science 2019)
Our research program uses numerousbiochemical and biophysical techniquesincluding protein expression and purificationsurface plasmon resonance and three-dimensional structure determination withthe use of the Australian SynchrotronFurther cellular immunology techniques aretaught within the laboratories ofcollaborators of the Rossjohn laboratory
The lab is funded by the National Health amp MedicalResearch Council the Australian Research CouncilNational Institutes of Health and The Wellcome TrustA large number of students and ECRs from the lab havebeen awarded various fellowshipshonours including thePremierrsquos award NHMRC PhD research scholarships CJMartin Fellowships Peter Doherty Fellowships and CDAfellowships ARC DECRA and Future fellowships EMBOfellowship NHMRC fellowships and Victoria Fellowships
1) Investigating lipid-based immunity in the context of Mycobacterium tuberculosis infection2) Investigating the role of lipids in skin-based allergies (eg contact hypersensitivities)3) A chemicalbiochemical study into vitamin B metabolite recognition4) Investigating T cell mediated autoimmunity (eg Celiac Disease)5) Investigating anti-viral immunity (eg SARS-Cov-2 HIV and Influenza)
RossjohnLab
theRossjohnLab
Nature Cancer 2020 Cover Bispecific nanobodies stabilize iNKT cell interactions for immunotherapy
Image Nanobodies targeting of a tumour cellArtwork Erica TandoriRead the full paper DOI 101038s43018-020-00111-6
41
Structural biology of Helicobacter pylori virulence factors Associate Professor Anna RoujeinikovaPhone 99029194Email AnnaRoujeinikovamonashedu httpmedmonasheduaumicrobiologyresearchroujeinikova
RESEARCH BACKGROUND
HONOURS PROJECTS
Helicobacter pylori is a causative agent of gastric and duodenal ulcers mucosa-associated B-cell lymphomaand gastric adenocarcinoma Although it is a definitive carcinogen there is no effective vaccine against thisbacterium Standard H pylori eradication therapy now fails in up to 30-40 of patients mainly due to anincrease in clarithromycin resistance There is a clear demand for new strategies to fight H pyloriinfections strategies that involve new or unconventional targets for drug design A key to success with thislies in strong basic knowledge of the molecular basis of bacterial virulence and survival Our laboratoryfocuses on the mechanisms of acid acclimation damage to gastric epithelial cells and motility andchemotaxis We use in vitro molecular biophysics and crystallography techniques to investigate structureand dynamics of biomolecules and formulate hypotheses about molecular mechanisms which we then testin vivo using genetics enzymology and cell biology methods
Dissecting architecture of high torque bacterial motor
How does H pylori sense environmental cues
Many bacteria are motile Chemotaxis mediated by chemoreceptors plays an important role in bacterial survival and virulence In this project we shall investigate what ligands such receptors recognize and why some molecules are attractants and some repellents how binding to the receptor leads to signalling how mutations in the sensor domain affect ligand specificity and building on this how bacterial chemoreceptors can be redesigned to recognize and respond to non-native ligands for innovative applications in biotechnology and bioengineering
Applications are welcome from students with a strong interest in structural biology X-ray crystallography the biology of H pylori or protein biochemistry
The bacterial flagellar motor is a remarkable nanoscale molecularengine H pylori evolved to be highly motile in the very viscousmucous layer of the stomach and its flagellar motor is specialised forlocomotion in viscous liquids ndash it produces a significantly highertorque (turning force) than for example enteric bacteria Preliminarycryo-electron tomography reconstruction of this motor revealed aunique protein cage that supports a wider power-generating ringallowing it to sustain the larger torque Our aim is to unravel themake-up of this cage and the structural basis for its ability to recruitmore force-generating units
42
Mitochondrial biology amp disease Professor Michael RyanPhone 9905 1670 Email michaelryanmonasheduwwwmonasheduaudiscovery-instituteryan-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Mitochondria produce ATP and other important molecules They also important in many other processesincluding apoptosis innate immunity and cell fate determination Defective mitochondria causedegenerative diseases and often lead to infant death We investigate the molecular and cellular processesrelated to mitochondrial function dysfunction and disease and dynamics Each student will perform arange of techniques attend weekly lab meetings and gain expertise for future scientific and non-scientificcareers Students will be mentored in the lab by one of our friendly postdocs Previous lab experience is notrequired but teamwork skills effective communication and a good work ethic is required
Understanding the function of novel humanproteins (with Drs Luke Formosa amp Boris Reljic)Complex I of the mitochondrial respiratory chainis a huge machine containing 44 differentsubunits Following up from our study (Stroud etal Nature 2016) we are identifying andcharacterising proteins involved in complex Iassembly and how their mutations cause diseaseWe wish to determine how specific mutations incomplex I subunits and assembly factors causedefects leading to disease by using CRISPRapproaches to generate cell models The studywill provide important new insights into anessential process
Investigating the importance of proteins inshaping mitochondria (with Dr Matt Eramo)Mitochondria form dynamic networks that rely onfission fusion and trafficking along thecytoskeleton Energy generating complexes insidemitochondria are also organised at mitochondriacristae Mitochondrial membrane shaping isgoverned by a number of protein machines Thisproject will investigate the importance of thesemachines and how they alter in activity inresponse to cellular cuesUnderstanding mtDNA escape during cell deathand disease (with Dr Kate McArthur)The mitochondrial genome resides in theinnermost compartment of the mitochondria butupon escape into the cytoplasm or extracellularspace it is a potent stimuli of the immune systemFollowing on from our study (McArthur et alScience 2017) we are examining the mechanismand contribution of mtDNA release duringdisease Using cutting-edge microscopytechniques this project will investigate how andwhy mtDNA is released from primary immunecells during disease
Techniques include CRISPRCas9editing DNA cloning tissue culturegrowth assays pull downs andproteomic analysis proteinfunction determination andwestern blot analysis tissuecellextractions flow cytometrymultiple different live-cell imagingtechniques including lattice light-sheet microscopy
43
Biochemistry Education ResearchDr Nirma SamarawickremaPhone 99020295 Email nirmasamarawickremamonashedu httpsresearchmonasheduenpersonsnirma-samarawickrema
RESEARCH BACKGROUND
Building Assessment Literacy Exploring Opportunities Across Large Courses (Nirma Samarawickrema)Monash University recognises that engaging students in assessment processes is central to the student learning experience For students to develop assessment literacy they need to understand the purpose of and process associated with assessment tasks to an extent that this translates into life-long learning The proposed study will explore the development of assessment literacy in selected courses of the University through an evaluation of (1) student and staff perspectives and (2) course material The finding of the study will inform learning designs that will ensure a betterlearning experience for students
An evaluation of active learning approaches adopted in the Biochemistry workshops (Nirma Samarawickrema)
This study evaluates the case study approach adopted in the Biochemistry workshops designed to connect theory to practice as well as develop graduate attributes
Please contact NirmaSamarawickremamonashedu for further information
HONOURS PROJECTS
Biochemistry Education Research uses quantitative and qualitative approaches to research into effective teaching assessment and curriculum design that leads to enhanced learning Our findings are used to improve curricula authentic assessments and student learning Adopting this strong evidence based approach ensures quality in teaching and learning
44
Mass spectrometry laboratoryProteomics Metabolomics and LipidomicsAssociate Professor Ralf SchittenhelmPhone 9905 4324 Email ralfschittenhelmmonashedu wwwmonasheduresearchinfrastructurempmf
RESEARCH BACKGROUND
HONOURS PROJECTS
Mass spectrometry has emerged as the leading technology to comprehensively identify and quantifyproteins and other biomolecules in virtually every biological sample
Our lab which is equipped with the latest mass spectrometric instrumentation focuses on utilizing andimproving mass spectrometry for biochemical and clinical research
All honours (and PhD) projects are highly technology-driven They are about applying establishing or furtherdeveloping state-of-the-art methodologies to addressfundamental questions in biomedical research andorto simplify mass spectrometric analyses
While a background in mass spectrometry orbioinformatics is beneficial it is not mandatory and wedo consider every studentrsquos interest and skill set to finda suitable project
The following projects are just a few examples which highlight the diversity of the available projects
1) Unravelling the interactome of Plasmodium falciparum using cross-linking mass spectrometry (CL-MS)Plasmodium falciparum is a unicellular protozoan parasite which causes malaria in humans In this project we will use CL-MS to unravel the global interactome of Plasmodium falciparum at various stages during infection with the goal to identifybiomarkers as well as targets for drug intervention
2) Development of a web application to visualize CL-MS data (Dry lab project)CL-MS is a cutting-edge technology to identify not only interacting proteins on a global scale but also interacting regionswithin proteins and protein complexes In this project an easy-to-use and automated web application should be developedto visualise and analyse such highly complex CL-MS datasets
3) Computer-aided decision support for interpreting complex lipidomics data (Dry lab project)Lipidomics is the large-scale study of cellular lipids in biological systems using mass spectrometry and indispensable to studythe onset and progression of a variety of medical disorders and diseases In this project we will aim to create accessibletools for the interpretation and downstream analysis of such complex lipidomics datasets
45
Nanoantibiotics LabDr Hsin-Hui ShenPhone 03 9902 9518 Email hsin-huishenmonashedu httpswwwmonashedudiscovery-instituteshen-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Lab head photo
Project 1 Cubosomes as smart nano-carriersThe key objective of this project is to functionalize cubosomes with S aureus targeting CARF peptide todevelop an active targeted delivery system Cubosomes will be conjugated with CARF peptides and thestructure of new formulation will be characterized using combination techniques such as dynamic lightscattering (DLS) cryogenic transmission electron microscopy (Cryo-TEM) and small-angle X-rayscattering (SAXS) The antimicrobial effect of CARF-functionalized cubosomes will be tested againsteight different strains of methicillin-resistant Staphylococcus aureus
Project 2 Modification of cubosomes as a new class of nanoantibioticAntimicrobial lipids serve as promising candidates for the treatment of MDR infections To improve thesolubility of antimicrobial lipids we will formulate some antimicrobial lipids into cubosomes as a newcombinational delivery system Three antimicrobial lipids (lauric acid capric acid and monolaurin) willbe formulated into cubosomes and characterized their size using DLS and morphology using Cryo-TEMSAXS will be performed to prove the structural composition of new formulations The antimicrobialeffect of those formulations will be tested against a variety of bacteria strains
The rise in antimicrobial multi-drugresistance (MDR) represents one ofthe greatest threats to humanhealth Many countries haveresponded with NationalAntimicrobial Resistance ActionPlans which have prioritised basicmicrobiological research to supportexisting antimicrobials as well asdevelop new antimicrobials adjuncttreatments and combinationtherapies
Nanomaterials have the great opportunity to serve as alternatives to antibiotics to control MDRinfections Cubosomes are self-assembled liquid crystalline nanoparticles composed of a uniqueinternal structure of lipid bilayers and aqueous channels Those channels provide a large internalsurface area for packaging of bioactive molecules such as antibiotics and antimicrobial peptides whichwill augment bacterial killing through improved drug delivery (Fig) Research in our lab will focus ondesigning new cubosomes formulations (withwithout bioactive molecules) and testing those newformulations on a wild range of MDR bacterial strains
46
Kidney development and diseaseProfessor Ian SmythPhone 9902 9119 Email iansmythmonasheduhttpswwwmonashedudiscovery-institutesmyth-lab
RESEARCH BACKGROUNDOur group studies how the embryo develops with a view to understanding the basis for congenital diseases and those caused by a compromised fetal environment In particular we are interested in understanding the developmental mechanism known as branching morphogenesis which is employed by a large number of organs to establish the tissue architecture required to facilitate exchange of nutrients gases or waste in the adult organ Understanding this process will provide insights into the developmental origins of congenital diseases and how the normal variations observed in the structure of organs are influenced by their experiences and exposures as an embryo
Project 1 Can we cure renal cysts by inhibiting Aurora kinase A
Abnormal kidney development is one of the most common birth defects We are pursuing a number of projects aimed at understanding their mechanistic and biochemical basis with a particular focus on renal cyst development and vesicoureteral reflux (VUR) One project in this area will focus on examining cyst development in the kidney and explore the interactions between the primary cilia-associated proteins INPP5E PKD1 and AURKA You will use mouse and cell based models of genetic deletion and pharmacological inhibition to study how polycystic kidney disease arises and the role these proteins play in its initiation and progression
Project 2 Characterising novel genes which cause congenital kidney disease
Our group is involved in an Australia-wide program which aims to identify novel genes in patients with kidney disease Individuals with genetic kidney disease who do not have mutations in known genes will These individuals will have their genomes sequenced and we will then use CRISPRCas9 genome engineering approaches to model disease causing mutations in mice Using these models honours students will have a unique opportunity to establish how novel disease genes function in the kidney how their protein products regulate cell biology and how their mutation leads to congenital renal malformations
HONOURS PROJECTS
47
CHEMOKINE-RECEPTOR INTERACTION Professor Martin StonePhone 9902 9246Email martinstonemonashedu httpswwwmonashedudiscovery-institutestone-lab
RESEARCH BACKGROUND
SIGNALLING MECHANISMS CONTROLLING RECRUITMENT OF WHITE BLOOD CELLS IN INFLAMMATIONIn this project we are studying the molecular details of how chemokines induce transmembranesignalling by their receptors and the intracellular signalling pathways that are activated by chemokine-receptor interactions These studies will provide a solid mechanistic foundation for future development ofselective therapeutic interventions
NATURAL ANTI-INFLAMMATORY PROTEINS CHEMOKINE INHIBITION BY TICK EVASINSTicks which live on mammalian hosts produce proteins called evasins which interact with hostchemokines and thereby prevent inflammatory responses allowing the ticks to live longer on their hostsWe have discovered a large number of new evasin proteins and shown that they bind and inhibit humanchemokines suggesting they have enormous potential as chemokine-targeted anti-inflammatory agentsThis research project focuses on characterising the interactions of evasins with chemokines Our resultswill enable the development of evasin-like proteins that target specific groups of chemokines ininflammatory disease therapy
TRAINING OPPORTUNITIESWe are seeking talented PhD Honours and undergraduate research students Students involved in theseprojects will develop high-level critical thinking project planning and communication skills as well as avariety of technical skills in biochemistry molecular biology pharmacology and bioinformatics
HONOURSPhD PROJECTS
Inflammation is the bodyrsquos response to injury or infection A key feature ofinflamed tissues is the accumulation of leukocytes (white blood cells) whichcarry out a variety of defence and tissue repair functions However excessiveor inappropriate leukocyte recruitment can give rise to the chronic pain andtissue damage observed in inflammatory diseases Leukocyte recruitment ininflammation is regulated by chemokines which are secreted at the site ofinjury or infection and then activate chemokine receptors G protein-coupledreceptors (GPCRs) expressed on the target leukocytes Research in our labaims to understand how the interactions of chemokines with their receptorscontrol leukocyte recruitment and to develop novel ways of suppressingthese mechanisms
48
CELLULAR SIGNALLING AND HUMAN DISEASE LABORATORYProfessor Tony TiganisPhone 03 990 29332 Email tonytiganismonasheduwwwmonashedudiscovery-institutetiganis-lab
PROJECTS ON OBESITY amp TYPE 2 DIABETES
PROJECTS ON OBESITY LIVER DISEASE amp LIVER CANCER
Excess body weight is a major and leading factor in overall disease burden worldwide and if left unabatedcould lead to falls in overall life expectancy particularly in developed nations such as the United States andAustralia In 2010 overweight and obesity were estimated to cause some 34 million deaths worldwideObesity is a key contributor to a myriad of human diseases including non-alcoholic fatty liver disease(NAFLD) and cancer Moreover obesity is the single most important contributor to the development of type2 diabetes a major cause of obesity-associated morbidity and mortality
The environmental epidemiological and socioeconomic factors underlying the development of obesity andtype 2 diabetes are multifactorial and complex Their increasing prevalence indicates that dietary andlifestyle interventions alone are unlikely to be effective in combating obesity and type 2 diabetes andunderscores the need for a better understanding of their aetiology and the development of noveltherapeutic approachesProjects are available to explore both Central Nervous System (CNS) and peripheral mechanismscontributing the development of obesity type 2 diabetes and their complications
Obesity is a leading factor in the development of liver disease with gt85 of overweight individualsdeveloping NAFLD NAFLD encompasses a broad spectrum of liver conditions ranging from simple steatosisto the more severe and progressive non-alcoholic steatohepatitis (NASH) a condition that results in fibrosisand if left unresolved cirrhosis (late-stage liver disease) andor liver cancer Obesity-associated NASH iscurrently the third leading cause for liver transplantation and is expected to soon surpass hepatitis C as theprincipal cause for liver transplantation and HCC in the developed world
Projects are available to determine the mechanisms by which obesity drives the development of NASHfibrosis and liver cancer
PROJECTS IN IMMUNO-ONCOLOGYTherapies that enhance the immune response to tumours have revolutionised the management of cancerHowever most tumours do not have a high mutational burden and are therefore not lsquovisiblersquo to theimmune system or evolve alternate immunosuppressive mechanisms to escape immune-surveillance As aconsequence such tumours remain largely unresponsive to current class-leading immunotherapiesincluding those targeting immune checkpoints Chimeric antigen receptor (CAR) T cell therapy has emergedas an exciting immunotherapy approach for lsquonon-immunogenicrsquo cancers as it does not rely on endogenousanti-tumour immunity CAR T cells are autologous T cells engineered to express a CAR specific for a tumourantigen CAR T cells targeting CD19 have transformed the treatment of acute lymphoblastic leukemia withclinical response rates of up to 90 However CAR T cells remain ineffective in solid tumours
Projects focussed on the development of next generation CAR T cell therapies for solid tumours areavailable
49
Emerging deadly infections building molecular knowledge for better therapiesProfessor Ana TravenPhone 9902 9219Email anatravenmonasheduhttpswwwmonashedudiscovery-institutetraven-lab
Fungal pathogens can escapefrom immune containment by producing invasive hyphae that lyse macrophages
RESEARCH BACKGROUND We study infections that threaten the lives of patients in intensive care cancer and surgical wards We utilise interdisciplinary approaches to solve this grand challengeIn the Western world few of us expect to die from an infection But if the current trends continue it is predicted that by 2050 as many as 10 million people might die every year from untreatable infections resulting from the raising resistance of pathogens to antibiotics Hospitalised COVID-19 patients are also at higher risk from secondary infections by bacteria and fungi This is convincingly demonstrated by the dramatic epidemic of ldquoblack fungus in India which has killed more than 4000 people to date
Our laboratory focuses on significant and emerging fungal pathogens We take a multi-pronged approach to (i) understand the biology of the fungi that promotes their survival in patients (ii) decipher how they evadeimmune responses and (iii) characterise compounds that could lead to novel antifungal therapies
We use a range of techniques to work on these questions from molecular cell biology and imaging to infection models and system-level ldquoomicsrdquo approaches Our Honours students are trained in broad and highly relevant skills that can be applied to a whole range of questions in biomedical science
Our lab is integrated into the Infection Research Program in the Biomedicine Discovery Institute the Monash-Warwick Alliance Training Program in Emerging Superbug Threats and the Monash Centre to Impact Antimicrobial Resistance (AMR) We work within these interdisciplinary programs to find improved solutions to deadly infections
HONOURS PROJECTS How do fungal pathogens evade immune responses (with Dr Harshini
Weerasinghe)We want to understand how fungal pathogens escape ad kill innate immune cells This knowledge will tell us how we could manipulate these pathways to favour an immune response that is able to control infections
Characterisation of novel antimicrobial compounds (with Dr Claudia Simm)We are working on characterising antifungal compounds that have activity against fungal pathogens for which few treatments exist This project involves antifungal drug susceptibility experiments combined with molecular cell biology biochemistry and chemical genetics approaches to discover the mechanisms of action
Recent publications from the lab1 Tucey et al Cell Metabolism 2018 v 27 988-10062 Tucey et al PLoS Pathogens 2020 v 16 e10086953 Koch et al Cell Reports 2018 v25 2244-22584 Wang et al Cell Reports 2020 v31 107528 50
Molecular ImmunologyDr Julian VivianPhone 99029240 Email julianvivianmonashedu httpswwwmonashedudiscovery-institutevivian-lab
Project 2 KIR3DL1 in acute myeloid leukaemia This project centres on KIR3DL1 polymorphism and how it translates to improved outcomes in hematopoietic stem cell transplantation for the treatment of haematological malignancy (Vivian et al J Exp Med (2016)) Combining functional and clinical data the aim is to understand KIR in donor selection for HSCT treatment of AML
Project 3 The activating receptor KIR2DS5 KIR2DS5 is an activating KIR that was long thought to be areceptor without a ligand We have recently identified the ligand for KIR2DL5 (unpublished) This project isan opportunity for the student to learn the structuralfunctional techniques listed above to validate thesepreliminary results and establish the framework for the field to understand KIR2DS5 This project is acollaboration with Prof Peter Parham Stanford Uni USA and Prof Andrew Brooks Melb Uni
HONOURS PROJECTS
The projects centre broadly on the role of Natural Killer Cell receptors in disease progression The projectswill focus on the role of KIR receptors in the control of HIV replication and progression of haematologicalmalignancies It is well established that KIR receptors are grouped into activating and inhibitory sub-typesthat together dictate the cellular immune response Yet how these two receptor sub-types differ in terms ofligand recognition and how this plays out with regard to sensing and controlling HIV infection and otherdiseases is unknown We are interested in characterising these receptors at the cellular molecular andatomic level See reference Vivian et al Nature (2011) 479401-5
Techniques and the LabThe projects will involve challenging and multi-disciplinary approaches They will provide an opportunity tolearn bacterial insect and mammalian techniques for protein expression Biophysical techniques for proteincharacterisation including small-angle X-ray scattering analytical ultracentrifugation surface-plasmonresonance and atomic resolution protein structure determination by X-ray crystallography Alsoimmunological techniques including cell culture and flow cytometry The laboratory is exceptionally wellfunded and well equipped and is host to a large number of helpful researchers with expertise in a diverseset of disciplines In all it provides an excellent research environment for students
Project 1 The enigmatic receptor KIR2DL5KIR2DL5 is the least understood member of theKIR family By sequence KIR2DL5 is a hybrid ofKIR3DL1 (see Vivian et al Nature (2011)479401-5) and KIR2DL4 (see Moradi and VivianJ Biol Chem (2015) 290(16) 10460ndash10471) YetKIR2LD5 has the properties of neither Thisproject will involve biophysical and functionalcharacterisation of KIR2DL5 This is a anopportunity for the candidate to learn proteinChemistry X-ray crystallography and SAXS The function of KIR2DL5 will be probed by cellular assays Thisproject is a collaboration with Prof John Trowsdale Cambridge Uni UK
RESEARCH BACKGROUND
51
Nuclear Therapeutics LaboratoryDr Kylie WagstaffPhone 03 99029348 Email kyliewagstaffmonashedu wwwmonashedudiscovery-institutewagstaff-lab
RESEARCH BACKGROUNDNuclear transport is critical to many cellular functions and during many disease states including viral infectiondementia and cancer can result in aberrant protein trafficking and deleterious effects on the cell For exampleduring cellular stress many proteins transition into and out of the nucleus to mediate transcriptional changesfacilitate DNA repair trigger cell cycle arrest and if the damage is high enough to stimulate apoptosis Theparadox being that under cellular stress conditions the normal pathways that facilitate protein movement intoand out of the nucleus do not function We have identified a novel nuclear transport pathway that continues tofunction under cell stress conditions the first such pathway to be defined Similarly many viruses hijack the cellsnuclear transport pathways either as part of their normal viral life cycle or to inhibit the cells innate anti-viralresponses We study these interactions between he virus and the host and use this knowledge to develop specificanti-viral therapeutics against them This program has led to two compounds currently under clinicaldevelopment against COVID-19 and Dengue fever
HONOURS PROJECTSProject 1 The role of nuclear transport factors in cellular stressDuring cellular stress conditions the nuclear transport proteins thatnormally mediate nuclear transport are mislocalised and rendered non-functional due to a collapse in the cellular Ran gradient We haveidentified a novel nuclear transport pathway that appears to play a rolein both the collapse of the Ran gradient in response to stress and therecovery of it afterwards Project 1 will examine this pathway in detailassessing the contribution of nuclear transport proteins and the responseto various stress conditions Techniques will include quantitativeconfocal laser scanning microscopy advanced single moleculemicroscopic techniques tissue culture KO stem cells protein-proteininteraction studies western blotting siRNA and immunofluorescence
Project 2 Identifying a novel stress-responsive nuclear transportpathway Our laboratory has recently identified a second a potentialnuclear transport pathway that is active under stress Project 2 willdefine this novel transport pathway for the first time and its role in thestress response Techniques will include tissue culture KO stem cellsprotein-protein interaction studies western blotting siRNA andimmunofluorescence
1 3216 48
Log
time
(s)
pCF(0) amplitude
Cyto Nuc
Project 3 Examining the nuclear transport of Coronavirus proteins as a potential therapeutic targetThis project will examine key proteins from COVID-19 and related viruses to determine their nuclearlocalisation Inhibitors of nuclear transport will be used to confirm pathways and the effect validated on viralinfectionTechniques include microscopy tissue culture viral infection plaque assays protein interaction assaysinhibition studies
Key Words Nuclear transport virus microscopy cells 52
The Whisstock LaboratoryProfessor James WhisstockPhone 0418 170 585Email JamesWhisstockmonashedu httpswwwmonashedudiscovery-institutewhisstock-lab
RESEARCH BACKGROUND
HONOURS PROJECTS
Professor James Whisstock is an Australian Laureate Fellow Director of the ARC Centre of Excellence inAdvanced Molecular Imaging and Scientific Head of EMBL Australia The Whisstock laboratory uses X-raycrystallography and cryo-electron microscopy cell biology biophysics techniques and monoclonaltechnology to study inflammation infection immunity blood clotting cell signaling and developmentalbiology
These studies are focused on knowledge-based research as well as the translation of such knowledge in thedevelopment of therapeutics and diagnostics for inflammation immune driven disorders cancerneurological disorders and thrombotic diseases
1 Improving the outcome of stem cell transplantation therapy (in collaboration with Dr Ruby Law)
2 Structure and function of pore forming toxins in the human immune system (in collaboration withAProf Michelle Dunstone and Dr Ruby Law)
3 Preventing the formation of pathological thrombi (in collaboration with Dr Ruby Law and Dr Alex deMarco)
4 Control of the plasminogen system in infection and wound remodeling (in collaboration with Dr RubyLaw and Prof Dena Lyras)
5 In situ structural studies of Drosophila embryogenesis (in collaboration with Dr Alex de Marco and DrTravis Johnson)
Perforin-like proteins drives the localization of growth factors in Drosophila embryogenesis through an unknown mechanism (Johnson et al Nature Comms 2015)
Cryo-EM Structure of the Macrophage pore formingProtein MPEG-1 (Pang et al Nature Comms 2020)
53
Wilce Lab ndash Protein-RNA interactionsProfessor Jackie WilcePhone 99029226 Email jackiewilcemonashedu httpswwwmonashedudiscovery-institutejackie-and-matthew-wilce-lab
RESEARCH BACKGROUNDProtein-RNA interactions in antiviral cellular defence and inflammationProtein-RNA interactions are integral to cellular biology ndash both in normal cellular function and also in cells subject to the stresses of viral invasion Our lab has specialised in the study of protein-RNA interactions using biophysical and structural tools to better understand the basis for their affinity specificity and conformational consequences underlying their mechanism of action Our objective is to delineate specific protein-RNA systems relevant to antiviral cellular defence
HONOURS PROJECTSProject 1 Structural characterisation of picornavirus RNAprotein complexesPicornaviridae family are positive strand RNA viruses with many members including enteroviruses human rhinoviruses encephalomyocarditis virus aphthoviruses and hepatitis A virus This family cause a range of significant diseases such as paralysis hand-foot-and-mouth disease the common cold myocarditis and hepatitis Replication of the viral RNA requires the formation of a specific interaction between viral ldquostem loop IVrdquo and poly-C-binding protein (PCBP) We are currently investigating the structural basis of this interaction that is required for ribosome docking of the viral RNA as a potential new anti-viral target
Project 2 TIA proteins in RNA recognition and stress granule formationOne of the cellrsquos primary rapid responses to stress is to sequester specific proteins and RNA into dense clusters known as ldquostress granulesrdquo (SGs) In this way the proteins and RNA are removed from their normal cytoplasmic sites of activity and held at bay until the stress is relieved This process is essential for regulating the expression of pro-inflammatory proteins as well as stress-response proteins and oncoproteins Accordingly improper SG formation is implicated in many pathologies including inflammation and cancer and neurodegenerative diseases We are currently investigating the way in which TIA proteins recognise RNA and self-associate to form stress granules
These (and other projects in the Wilce lab) are currently supported by NHMRC and ARC funding Please come and speak to us to find out more
PCBP2SLIV complex
TIA-1oligo complex
stress granules
54
Epigenetics and Chromatin ResearchAssociate Professor Lee WongPhone 03 99024925 Email leewongmonasheduhttpswwwmonashedudiscovery-institutelee-wong-lab
RESEARCH BACKGROUNDEpigenetics is the study of changes in gene activity that donot involve alterations to the DNA Examples of epigeneticmechanisms are DNA and histone methylation histonevariants and noncoding RNA Our research interest is toidentify new chromatin factors that control genetictransmission and DNA stability We investigate genome-wide epigenetic defects associated with chromatin factorATRX and histone variant H33 mutations in brain cancers
HONOURS PROJECTS
Roles of histone H33 mutations in driving chromatin abnormalities in brain cancers
The nucleosome forms the basic unit of chromatin and is critical for regulating and protectinggenomic DNA Each nucleosome is comprised of 146 bp of DNA wrapped around an octamer ofhistone proteins two units each of H2A H2B H3 and H4 Mutations in chromatin proteins makethe genome vulnerable to mutations and results in genome instability which is a key early event incancer Oncogenic chromatin mutations can occur on chromatin readers writers erasers and onthe nucleosome
The most common brain cancer in young people - particularly under the age of 15 years - is calledGlioblastoma multiforme (GBM) This is an aggressive stage four brain tumour formed in theupper part of the brain that invariably leaves young patients with just over a year to live Little isknown about the underlying causes of why GBM forms - which in turn has hampered thedevelopment of treatments that specifically target GBM tumours Recent studies show thatHistone point mutations are frequently found in GBM and the majority of these point mutationsoccur on histone variant H33 This project investigates how mutated H33 proteins affect genomestability (telomere function) and chromatin inheritance (gene expression and cell differentiation)
Techniques Embryonic stem cell culture and differentiation cell culture immunofluorescenceWestern blotting CRISPR Cas9 DNA targeting and editing FISH (fluorescence in situ hybridization)chromatin immunoprecipitation proteomics and real-time PCR analyses
Staining of telomeric (green) and peri-centromeric (red) repetitive DNA in mouse cells
55
Laboratory of Mucosal Immunity and InflammationProfessor Colby ZaphPhone 99050783 Email colbyzaphmonashedu wwwzaphlabcom
RESEARCH BACKGROUNDThe overarching goal of research in the Zaph lab is to define the cellular and molecular mechanisms that control immunity and inflammation at mucosal sites such as the intestine and the lung The various subsets of immune and non-immune cells at mucosal sites are present in a tightly controlled equilibrium that when perturbed by infection chemicals or genetic predisposition results in dysregulated inflammation and diseases including asthma and allergy inflammatory bowel diseases (IBDs) food allergies and cancer Understanding the molecular and cellular principles underlying mucosal inflammation represents a potential target for identifying novel therapeutics for the treatment of these diseases
Project 1 Epigenetic regulation of mucosal immunity and inflammationWe have been at the forefront of defining the epigenetic mechanisms thatcontrol T cell differentiation and function (Lehnertz (2010) J Exp MedAntignano (2014) J Clin Invest) focusing on lysine methyltransferases(KMTs) enzymes that methylate histones to repress or activate geneexpression This project involves the characterization of the epigenomicregulators of T cell physiology and will focus on linking genome-wide histonemodifications (via ChIP-Seq) to functional assays in vivo
Project 2 Retinoic acid Hic1 and intestinal immune homeostasisMicronutrients such as Vitamin A (and its derivative retinoic acid (RA)) play acritical role in intestinal immune homeostasis However the molecularmechanisms that link RA signaling to immune cell function in the gut areunclear We have recently identified a role for the transcriptional repressorHic1 as an RA-responsive gene that controls intestinal immune cellhomeostasis and function This project will use novel mouse models todefine the role of Hic1 in immune cells during the steady state and followinginfection and inflammation
Project 3 Methylation is the new phosphorylation Dynamic regulation ofsignal transduction by methylationWe have recently identified a novel role for the methyltransferase SETD7 inregulation of the HippoYAP signalling pathway (Oudhoff (2013) Dev CellBarsyte-Lovejoy (2014) Proc Natl Acad Sci USA) We have now extendedthese findings to show that SETD7YAP interactions control activation of theWntβ-Catenin pathway and regulate intestinal regeneration andtumourigenesis This project will define how SETD7-dependent methylationcontrols Wnt-dependent processes in the intestine
HONOURS PROJECTS
56
Epigenetics and Gene Regulation GroupDr Qi ZhangPhone 9902 9339 Email qizzhangmonasheduhttpsresearchmonasheduenpersonsqi-zhang
RESEARCH BACKGROUND
HONOURS PROJECTS
Key research methods biochemistry and biophysics structural biology (cryo-electron microscopyand X-ray crystallography) proteomics cell culture bioinformatics
Epigenetic marks regulates gene expression and someof these marks are created by histonemethyltransferase My research interest is focused ontwo key histone methyltransferases the H3K9methyltransferase G9A and the H3K27methyltransferase PRC2 (the polycomb repressivecomplex 2) G9A and PRC2 are essential for normaldevelopment and are dysregulated in cancer andcongenital disorders therefore they are consideredpromising targets for novel therapeutics with severaldrugs under development and one that was recentlyapproved (Tazemetostat)My research is to identify new functional centres that regulate G9A and PRC2 and provide newtargets for novel therapeutics Our group is part of the Epigenetic Regulation Structure and FunctionLab (led by AProf Chen Davidovich) and our recent publications include the identification of theRNA-binding site on PRC2 [Zhang et al Nat Struct Mol Biol 2019] and the discovery of a newallosteric regulation pathway on PRC2 [Zhang et al Nat Comm 2021]
Project 1 How G9A and PRC2 are regulated by their cofactors and shared subunitsThis project will utilize reconstituted protein complexes to determine how G9A and PRC2 areregulated by their cofactors and shared subunits at molecular level using cryo-EM crystallographymass spectrometry and in vitro binding and enzymatic assays
Project 2 Investigate the functional importanceof G9A and PRC2 regulation through theircofactors and shared subunits in embryonic andcancer cellsThis project aims to determine the functionalconsequence of G9A and PRC2 regulationthrough their cofactors and shared subunitsthrough approaches such as CRISPR flowcytometry proteomics and next generationsequencing
57
- Cover Page
- Table of Contents 1
- Table of Contents 2
- How to enrol in Honours
- Aguilar Prof Mibel
- Beilharz AProf Traude
- Bird Prof Phil
- Boag Dr Peter
- Cole Prof Tim
- Coulibaly AProf Fasseli
- Croft Dr Nathan
- Cryle AProf Max
- Davey Dr Martin
- Davidovich AProf Chen
- De Marco AProf Alex
- Dunstone AProf Michelle
- Ellisdon Dr Andrew
- Fletcher Dr Anne
- Huntington Prof Nicholas
- Illing Dr Patricia
- Jacobson AProf Kim
- Jans Prof David
- Knott Dr Gavin
- Kwok-Schuelein Dr Terry
- La Gruta Prof Nicole
- Lahoud AProf Mireille
- Law Dr Ruby
- Lazarou Dr Michael
- Le Nours Dr Jerome
- Mifsud Dr Nicole
- Mitchell Prof Christina
- Naderer Dr Thomas
- Nguyen Dr Lan
- OKeeffe AProf Meredith
- Papa Dr Antonella
- Purcell Prof Anthony
- Ramm AProf Georg
- Reid Dr Hugh
- Rose Dr Adam
- Rosenbluh AProf Sefi
- Rossjohn Prof Jamie
- Roujeinikova AProf Anna
- Ryan Prof Michael
- Samarawickrema Dr Nirma
- Schittenhelm AProf Ralf
- Shen Dr Hsin-Hui
- Smyth Prof Ian
- Stone Prof Martin
- Tiganis Prof Tony
- Traven Prof Ana
- Vivian Dr Julian
- Wagstaff Dr Kylie
- Whisstock Prof James
- Wilce Prof Jackie
- Wong AProf Lee
- Zaph Prof Colby
- Zhang Dr Qi
-
