The CCT is a network of advanced core facilities connected to the 12 research units and the translational department of the Institut Curie Research Centre offering state-of-the-art technol-ogies. In a unique constellation of expertise, the CCT combines technical know-how and develop-ment to tackle biological questions, ranging from basic to more applied, with a focus on cancer biology and treatment. Our highly trained, motivated staff works closely with researchers and clinicians to foster a creative environment where innovation can thrive. To keep up-to-date and provide the best service and newest techniques to our investigators we are constantly on the lookout for upcoming technologies through our TechWatch programme.It aims to bring together developers of technical solutions and scientific experts, such as recently on data management solutions and single cell technologies.We particularly support junior groups to develop their research and we train PhDs, postdocs and technical staff in the most advanced techniques. The CCT is open to reciprocal collaborations with sister institutions giving access to each other’s facilities to complement resources and efforts, and to exchange expertise and best practices.

The success of the CCT is rooted in an exceptionally strong culture of developing tools linked to discovery research. This provides the foundation for a seamless translation of applications into basic cellular and molecular studies with the ultimate aim to reach clinical application and patient care. The development of ground-breaking imaging technologies and Next Generation Sequencing tightly linked to bioinformatics and data analysis, are examples of this culture.

In the words of our director, Geneviève Almouzni: ‘At the CCT, “the Curie’osity’ of all our colleagues ensures a Constantly Creative Technological support that is always evolving’.The CurieCoreTech plays a key role in making Institut Curie a leading research institute and an attractive place to work – come and join us!

Andrea Hutterer, PhDCoordinator, CurieCoreTech

to the CurieCoreTech (CCT)Welcome

We offer access to cutting-edge technologies and exceptional service in a harmonised and cost-effective manner. We also provide comprehensive user training to support research at the forefront of scientific and medical advance.

Platform Type 1

· Affiliated to research unit· Dedicated platform manager · Scientific guidance from unit

Platform Type 2

· Translational gate· Dedicated platform manager · Guidance from Head of TRD*

Platform Type 3

· Within research centre· Dedicated platform manager · Guidance from institute director

• 9 technology platforms• 5 translational gates• 2 in-house services• 1 resource

‘A core coordination’ (Andrea Hutterer, Coordinator CurieCoreTech)

* Translational Research Department

nanoSpray ion source; AB SCIEXTM TripleTOF® 6600 MS

CELL & TISSUE IMAGINGOptical MicroscopyElectron MicroscopyChemical ImagingIn-house service: Histology

GENOMICSNext Generation SequencingGenomics

PROTEOMICSMass Spectrometry & ProteomicsProtein Expression & Purification Therapeutic Antibodies (TAb-IP) & Recombinant AntibodiesReverse Phase Protein Arrays

HIGH THROUGHPUT SCREENINGBiophenics ScreeningSynthetic Genetic ArraysResource: Chemical Library

CYTOMETRYFlow Cytometry Paris & Orsay

IN VIVO EXPERIMENTATIONLaboratory of Preclinical InvestigationExperimental RadiotherapyIn-house service: Animal Facility (in vivo experimentation)

BIOINFORMATICSBioinformatics

ASSOCIATED PLATFORMIPGG-Microfluidics

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The CurieCoreTech technological platforms fall into eight categories. They address biological questions ranging

from small molecules to whole organisms with state-of-the art equipment to respond to

the demands of an international research centre.

Funding & Partners

Institut Curie combines a research centre and a hospital group into a world-class, comprehen-sive cancer centre for multidisciplinary international research and cutting-edge cancer medicine.

The research centre, under the direction of Geneviève Almouzni, comprises 12 joint research units, which are structured around four thematic domains, each covering three units, with the objective to promote strong research orientations, interdisciplinarity and collaboration. Domain 1. Biology and Chemistry of Radiations, Cell Signalling and Cancer Domain 2. Biology, Cancer, Genetics and Epigenetics Domain 3. Tumour Biology, Immunology and Environment Domain 4. Multi-scale Physics-Chemistry-Biology and Cancer

These four highly interactive domains are linked by the CurieCoreTech technological platforms and the advanced training unit. The translational research department serves as a further catalyst for cross-domain activities, actively connecting the research centre to clinical research and facilitating a seamless interaction with the Hospital Group. The research centre creates a vibrant environment in which creative research can thrive and meet the scientific challenges of today’s cancer research.

Tailor made program for all at each step of their careerTowards the future: A trainee is a trainer

training.curie.fr

Training & Education are tightly linked to our research & our technological development

International interactions are in the fabric of the Institut Curie Research Centre*

© A Lescure/ M Thevenet

* International networks and consortia, institutional partnerships, European programmes (H2020),international collaborations resulting in joint publications.

© Musée Curie

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The platform services cover the entire range of biological complexity from small molecules up to whole organisms, and contribute to the progress of basic and translational research projects up to clinical studies. Together with the existing strong interactions among the platforms and the available access to patient samples via the hospital, this allows the use of the Curie CoreTech as a pipeline, a feature particularly attractive to external partners, as it enables the realisation of projects to a large extent in-house. Coordination of the CCT platforms and services under the oversight of a dedicated coordinator, Andrea Hutterer, is key to the success of this unique structure. The coherent organisation, harmonised functioning and systematic alignment with the research centre’s scientific vision paired with the openness at the international level allows the CCT to set the standard to the highest level of science and technologies.

For further information, contact Andrea Hutterer (andrea.hutterer@curie.fr), CurieCoreTech Coordinator.

The NGS, Genomics and Bioinformatics platforms are integrated into the France Genomique network, the Cell&Tissue Imaging Facility is part of the national infrastructure FranceBioImag-ing and by extension the European Research Infrastructure EuroBioImaging, and the Labora-tory for Preclinical Investigation is an active member of the EurOPDX consortium for patient derived xenografts, which gathers 16 cancer centres and universities across 10 European countries.

The Curie-CoreTech brings together the central technology platforms of Institut Curie and provides its researchers with access to state-of-the-art equipment and expertise in a cost-effec-tive manner. The platforms manage access, provide service support, the latest scientific know-how, and in some cases develop technologies as well. Each platform is headed by a highly experienced platform manager, who is expert in the technology offered and responsible for the day-to-day operations. The platforms are strongly linked to the research groups of the research centre. This allows them to remain responsive to the fast evolving scientific advances.The Curie-CoreTech consists of 16 technology platforms, five of which are part of the translation-al research department (‘translational gates’) and two of which are in-house services; and an additional resource, the chemical library. Users also have access to the microfluidic platform of the Institut Pierre-Gilles de Gennes (IPGG). Apart from the in-house services, all platforms are open to external users from both academia and industry and many successful collaborations and partnerships have been established. To highlight but one, the Cell & Tissue Imaging platform hosts one of only nine Nikon Imaging Centres world-wide and the sole one in France.

Importantly, Institut Curie is a member of EU-Life , an alliance of 13 top research centers in life sciences with the aim to support and strengthen European research excellence to which the CCT contributes at the level of core facilities. The individual platforms are also well connected and embedded in several national and international networks and initiatives.

Industrial Partners

Hospitalaccess to samples, translational researchclinical trials

Researchlinked with units, joint grant applications

TechWatchdevelopment & innovation

TrainingNetworksnational &international

Academic partners & cooperationsPSL, IPGG*, Institut Pasteur, Centre Léon-Bérard

Flow Cytometry

Electron Microscopy Chemical Imaging

Optical Microscopy Small animal facilityMicroscopyRadExpHistology

Chemical LibraryChemical Imaging

Bioinformatics

Mass SpectrometryProtein Expr. & Purific.

RPPATAb-IP & Rec. Abs

BioinformaticsBioinformatics

Next GenerationSequencing

GenomicsSGA

Bioinformatics

Smallmolecules

Genome Proteome Cells & Tissues Animal models &humans

Bioinformatics

* PSL: Paris Sciences et Lettres research university; IPGG: Institut Pierre-Gilles de Gennes

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Babraham Institute; Biotech Research and Innovation Centre (BRIC); Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM); Center for Genomic Regulation (CRG); Central European Institute of Technology (CEITEC); European Institute of Oncology (IEO); Friedrich Miescher Institutefor Biomedical Research (FMI); Institute for Molecular Medicine Finland (FIMM); Institute Gulbenkian de Ciencia (IGC); Max Delbrück Center (MDC); The Netherlands Cancer Institute (NKI); VIB

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The CurieCoreTech platforms make an essential contribution to the publication output of the research centre. Their support ranges from basic ‘fee-for-service’ to advice on methodologies to be employed, significant input on experimental design and writing of the manuscript.

Recent publications with platform participation include:

Mass spectrometry and proteomicsProteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes. Kowal J, Arras G, Colombo M, Jouve M, Morath JP, Primdal-Bengtson B, Dingli F, Loew D, Tkach M, Théry C.Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):E968-77.

Therapeutic Antibodies (TAb-IP) & Recombinant AntibodiesNaLi-H1: A universal synthetic library of humanized nanobodies providing highly functional antibodies and intrabodies.Moutel S, Bery N, Bernard V, Keller L, Lemesre E, de Marco A, Ligat L, Rain JC, Favre G, Olichon A, Perez F.Elife. 2016 Jul 19;5. pii: e16228.

RPPAIntegration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer. Michaut M*, Chin SF*, Majewski I*, Severson TM*, Bismeijer T*, De Koning L*, Peeters JK*, Schouten PC, Rueda OM, Bosma AJ, Tarrant F, Fan Y, He B, Xue Z, Mittempergher L, Kluin RJC, Heijmans J, Snel M, Pereira B, Schlicker A, Provenzano E, Raza Ali H, Gaber A, O'Hurley G, Kay E, Lehn S, Muris JJF, Wesseling J, Sammut SJ, Bardwell HA, Barbet AS, Bard F, Lecerf C, Vis DJ, Benes CH, McDermott U, Garnett MJ, Simon IM, Jirström K, Dubois T, Linn S, Gallagher WM, Wessels LFA, Caldas C, Bernards R (*co-first authors)Nature Sci Rep. 2016 Jan 5;6:18517

Cell & Tissue ImagingReal-Time Tracking of Parental Histones Reveals Their Contribution to Chromatin Integrity Following DNA Damage.Adam S, Dabin J, Chevallier O, Leroy O, Baldeyron C, Corpet A, Lomonte P, Renaud O, Almouzni G, Polo SE.Mol Cell. 2016 Oct 6;64(1):65-78

Biophenics ScreeningFunctional assessment of genetic variants with outcomes adapted to clinical decision-making.P Thouvenot, B Ben Yamin, L Fourrière, A Lescure,T Boudier, E Del Nery, A.Chauchereau, D Goldgar, C Houdayer, D Stoppa-Lyonnet, ANicolas, Gaël A. Millot. PLOS Genetics 2016, 12 (6).

Laboratory of Preclinical InvestigationActivation of IFN/STAT1 signalling predicts response to chemotherapy in oestrogen recep-tor-negative breast cancer.Legrier ME, Bièche I, Gaston J, Beurdeley A, Yvonnet V, Déas O, Thuleau A, Château-Joubert S, Servely JL, Vacher S, Lassalle M, Depil S, Tucker GC, Fontaine JJ, Poupon MF, Roman-Roman S, Judde JG, Decaudin D, Cairo S, Marangoni E.Br J Cancer. 2016 Jan 19;114(2):177-87.

GenomicsUveal melanoma cells are resistant to EZH2 inhibition regardless of BAP1 status.Schoumacher M, Le Corre S, Houy A, Mulugeta E, Stern MH, Roman-Roman S, Margueron R. Nat Med. 2016 Jun 7;22(6):577-8.

Mission and activity

Genomics, sequencing, high-throughput, ChIP-seq, RNA-Seq, whole exome sequencing

Services

ManagerDr Sylvain Baulande

ManagerDavid Gentien

The ICGex NGS platform offers state-of-the-art sequencing services for the research teams of the institute and to external customers. The platform also provides technical and scientific support in experimental design and sequencing strategies.Multiple sequencing protocols, mainly based on Ilumina technology, have been developed and are routinely used to perform most commonly used applications in genetics and epigenetics (genome, exome and targeted resequencing, RNA sequencing, DNA methylation sequencing, ChIP-seq, etc). The platform also co-develops specific protocols with research teams of the institute according to their needs. Latest upgrades include single-cell RNA-seq based on the C1 Fluidigm system and Drop-Seq technology from 10XGenomics. Currently, long-read sequencing approaches using the Sequel sequencer from PacBio are being implemented.The platform is not restricted to fundamental research and is involved in multiple translational research projects. Molecular characterization of clinical samples within a few days allows clinicians to evaluate the best therapeutic options for patient care.

• Whole genome, whole exome and targeted resequencing• Transcriptome analysis (RNA-seq for mRNA, total RNA and small RNA)• Epigenetics with DNA methylation, ChIP-seq for histone modifications or protein binding analysis and chromosome conformation capture approaches• Single-cell RNA sequencing• Long-read sequencing• Bioinformatics support through a Galaxy user-friendly interface (U900)

Genome, transcriptome, Nanostring nCounter® technology, Affymetrix microarrays

Mission and activityThe Genomics platform provides basic, translational, and clinical research teams with high- throughput technological tools for analysing gene structure and expression in various organisms, cellular models, and tumours. Structural genomic alterations, such as mutations, gains, amplifications, loss of genomic regions, polymorphisms, allelic imbalances, and loss of heterozygosity can be analysed through various state-of-the-art methods. Gene expression is complex and can be addressed at multiple levels: via the coding transcripts for proteins, exons (Affymetrix chips for pan-genomic analysis, or using NanoString multiplexing), or via qPCR depending on the number of samples and markers to quantify. The platform analyses the regulation of gene expression by quantifying microRNA, non-coding functional RNA, and other specific types of RNA, which modulate gene expression at both transcriptional and translational level. Such quantifications are performed by using Affymetrix chips or via NanoString multiplexing. Techniques for quantifying epigenetic markers are currently being tested (e.g. OxBS method developed by Cambridge Epigenetix).

In addition, the platform is taking part in several clinical trials in the field of cancer and rare diseases. DNA and RNA are analysed on a daily basis on dedicated tools such as Oncoscan and Cytoscan assays from Affymetrix, and the Prosigna assay from NanoString. As of 2016, the platform is in fact an authorized back-up laboratory for Prosigna assays in Europe due to its significant expertise, reliable service, and close interactions with NanoString Technologies Inc.

The platform is also participating in international projects and collaborations with partners from industry.

Services

Our platform provides dedicated support for genomics analysis for researchers and clinicians

• Advice in genomics analysis, experimental set-up• Sample preparation (cryo-sectioning, laser microdissection, nucleic acid purification)• Genome analysis (genome wide, based on arrays, or specific to hotspots, Sanger sequencing, methylation analysis)• Transcriptome analysis: genome wide, or customized up to 800 targets (Nanostring approaches)• Regulome analysis: miRNA and ncRNA, analysed with arrays or using Nanostring tools

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Next generation sequencing technology has now reached tremendous throughput and accuracy that enable researchersto conduct large-scale genomic projects at affordable cost and in less time.

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Scientific advisorsDr Olivier Delattre (Director, U830 - Genetics and Biology of Cancer) &Dr Alain Nicolas (Team leader ‘Recombination and Genetic Instability’, UMR3244)

The platform is part of the national genomics infrastructure France GénomiqueThe platform is part of the national genomics infrastructure France Génomique

Translational gateAffiliated with Translational Research Department (Head: Sergio Roman Roman)

NanoString PrepStation

DNA interaction matrix from Chr6 of a Uveal Melanoma tumor. (D Gentien, N Servant, et al.)

Genomics

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Mass spectrometry, high resolution, proteomics, post-translational modifications, interactions, quantitative mass spectrometry

Recombinant proteins, expression vectors, expression host development,protein purification, process development

Services• Protein and peptide identification• Comparison of proteomes• Analysis of post-translational modifications (localization and characterization)• Targeted proteomics• Quantitative proteomics (isotope labelling and label free)• Data processing• Bioinformatics and statistical analysis

Mission and activityThe Protein Expression & Purification platform is a service to overcome bottlenecks in recombi-nant protein expression and production. Any protein may present unique difficulties in obtaining a certain quantity, stability, or solubility; factors essential for its activity. Over the years, the platform has accumulated vast expertise in the production of secreted, nuclear, and membrane proteins by optimising different expression vectors in combination with appropriate cell culturing conditions. The platform offers equipment and material required for the expression of proteins in bacterial, yeast, insect and mammalian cells. The platform carries out entire projects, from cloning, expression, and scale-up to purification. Alternatively, the platform can be used to perform only specific tasks within a purification project. Part of the platform’s activities are dedicated to development and optimisation of new expres-sion systems and vectors. Optimising the gene sequences to be produced is a key step in the success of a project. To achieve it, multiple expression vectors have been developed and the combination of these genetics tools with optimised cell culturing conditions has allowed the successful completion of a vast number of protein production projects.

Training is provided for students and scientists in gene cloning and recombinant protein produc-tion and advice and active support for recombinant protein production using prokaryotic and eukaryotic expression systems is readily provided.

Services

The platform has expertise in all the classical expression systems and is continuously striving to optimise protocols and implement novel techniques.

ManagerDr Ahmed El Marjou

ManagerDr Damarys Loew

Mission and activityThe Mass Spectrometry & Proteomics facility platform provides the technical service and know-how to analyse proteins by mass spectrometry. One of the most promising approaches is to combine qualitative and quantitative analysis in a single analytical run adapted to the respec-tive research samples to achieve high sensitivity and low-level quantitation. The goal is to enable our collaborators to address scientific hypotheses more quickly and to functionally validate quanti-fied candidates.

The platform pursues two main applications: 1) Discovery-based (‘shotgun’) proteomics to detect proteins in complex mixtures. This is the standard approach to monitor protein content or post-translational modification enrichment in biological samples leading to the discovery of protein biomarkers. 2) Targeted proteomics for the accurate measurement of protein targets in biological samples. This allows to elucidate the molecular mechanisms of cellular functions via intricate protein networks and pathways.

The platform offers to its users personalized training to realise parts of the analyses as well as advanced training on all aspects of proteomics. The significant methodological expertise allows to advise on defining scientific questions, experimental design, sample preparation, data analysis and processing.

In collaboration with the Bioinformatics platform, tools for data management, mining, curation, and mass spectrometry-based data sharing are being developed. • Primer design and expression vector cloning

• Strain development• Expression screening• Protein production and purification• Preparation and distribution of recombinant expression vectors• New vector development to provide state-of-the-art expression technologies• Protein purification technology development

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Over the past years, mass spectrometry has made tremendous progress in sensitivity, high-throughput and depth of proteome analysis. Many assays beneficial for clinical and population studies have been developed.

Scientific advisorDr Bruno Goud (Director, UMR144 - Subcellular Structure and Cellular Dynamics)

Thermo ScientificTM UltimateTM 3000 RSLCnano LC system & Orbitrap FusionTM TribridTM MS

Single-domain antibodies, phage display screening, recombinant antibodies(rAb)

Protein arrays, proteomics, cell signalling pathways, phosphoproteins, translational research,biomarkers, patient classification

ManagerDr Leanne de Koning

Mission and activity

Services

The platform was created by two group leaders at Institut Curie, Franck Perez and Sebastian Amigorena, and has been operational since March 2012. Today, the platform collaborates with other research groups and platforms, both within the institute and externally, and also has contracts with industrial partners.

Antibodies are complex proteins used by the immune system to detect and neutralize pathogenic agents in a targeted manner. Using current technologies, we can identify antibody fragments in vitro by mimicking the immune system's own strategies of selection and amplification. Repertoires of antibody fragments can be expressed on the surface of bacteriophages and selected for their ability to bind the antigen (antibody phage display). This technique takes just 10 days to produce specific rAb without the use of laboratory animals.The platform uses a proprietary antibody phage display library based on a humanized nanobody scaffold that can provide high affinity binders circumventing the need for animal immunization. The library currently contains over 3 billion independent nanobodies (Moutel S., et al, eLife, 2016).

The platform focusses on four main themes:• Identification of antibodies for known antigens (basic research or therapeutic)• Isolation and characterization of antibodies specific for new cancer markers• Development of technologies for optimising the antibody-dependent imaging and drug delivery• Development of nanobodies usable for T cell engagement

Mission and activity The overall objective of the RPPA platform is to provide new biological insight on the protein level, with the ultimate goal to improve the treatment and the outcome of cancer patients. The platform takes part in diverse projects, ranging from fundamental research to clinical trials. A tailored, high-throughput, proteomic analysis of samples provided by collaborators is offered and permits the • Analysis of protein expression levels • Analysis of cell signalling pathway activation status and dynamics • Identification of prognostic or predictive protein biomarkers • Classification of (patient) samples according to their protein status • Integration of genomics, transcriptomics and protein data

Reverse phase protein arrays represent an innovative technology that allows studying protein expression levels and the activation status of cell signalling pathways. It combines high through-put analysis with minimal sample consumption. Using a dedicated printer, only 1 ng of proteins extracted from tissues or cell lines is printed onto nitrocellulose covered microscope slides, i.e. the arrays. Proteins of interest are then quantified using highly specific primary antibodies. Up to one thousand samples can be analysed simultaneously on the same array.Due to the small amount of biological material required, the technique is particularly suitable for the analysis of precious samples such as human biopsies, xenografts and flow cytometry sorted cells.

Our platform has validated over 600 primary antibodies for RPPA labelling so far. These include 150 antibodies against phosphorylated proteins, which cover the majority of cell signalling pathways.

Full in vitro selection of recombinant antibodies allows fast selection of humanized nanobodies directed against various type of antigens expressed by normal or by tumour cells.

Services• Validation of new primary antibodies• Sample preparation • Array creation & labelling with antibody of choice• Scanning and quantification of the signal• Data normalization• Exploratory data analysis (PCA and Hierarchical Clustering) and differential data analysis according to the scientific questions• Participation in writing of grant applications, reports and manuscripts

• Screening programs against identified targets.• Screening against the cell surface of a particular cell type.• In addition, the platform distributes ‘generic’ antibodies such as: - Anti-peptides (or "tag": myc, HA, ProtC, VSVG, etc.) - Antibodies produced from hybridoma (e.g. TfR, VSVG); recombinant forms with various Fc are also available. - Antibodies identified by the platform (e.g. anti-GFP, tubulin, etc.); multiple Fc species are available.

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Scientific advisor Dr Franck Perez (Team leader ‘Dynamics of Intra-Cellular Organization’, UMR144)

Translational gateAffiliated with Translational Research Department (Head: Sergio Roman Roman)

2470 Microarrayer-Aushon BioSystems

Manager Dr Sandrine Moutel

Hierarchical clustering based on RPPA data

Bio-imaging, image analysis, correlative light and electron microscopy, cryo-electron microscopy, molecular and 3D imaging, nanoSIMS, STEM, EFTEM, light microscopy, chemical imaging

Optical microscopy (Paris & Orsay)

The Optical Microscopy platform is distributed over four distinct buildings in both, Orsay and Paris, and the Nikon Imaging Centre. The facility is equipped with more than 40 advanced microscopic set-ups and assists about 300 users per year, including external users from acade- mia and the private sector.

ManagersDr Vincent Fraisier, Dr Olivier Renaud, Dr Patricia Le Baccon, Dr Marie-Noëlle SolerLucie Sengmanivong(Nikon Imaging Centre)

Overall mission and activityThe Cell & Tissue Imaging platform (PICT) brings together highly sophisticated equipment and up to date technologies in advanced microscopy. The objective is to provide research groups from inside and outside the institute with state-of-the-art imaging approaches to study at different levels and with complementary methods, molecules, organelles, cells, whole organisms and tissues in normal and pathological states.

For scientific and technical reasons, the platform is set-up as a multi-site facility with equipment and expertise located in different departments of the Institut Curie in Paris and in Orsay.

The platform is organized into three sections: • Optical microscopy • Electron microscopy • Chemical imaging

These different approaches allow users to delineate biological questions at different spatial and temporal scales from nanoscopy up to whole animal imaging.

The platform team teaches and trains users and is responsible for continuous evaluation of new available systems and technologies. A further part of the mission is to anticipate new challenges as new biological questions appear. Thus, there is a constant need to develop valuable and accurate solutions for all users, which include biologists, biophysicists, physicists and physicians. The platform is strongly involved in developing new hardware, applications and software solutions. Consequently, most platform members participate in R&D activities. The platform staff also organizes and teaches at national and international training courses and workshops.

The Cell & Tissue Imaging platform has been officially recognized with the IBiSA quality label for French national platforms since 2003. FranceBioImaging The platform is a member of France BioImaging, the national research infrastructure for biological imaging, which in turn is the unique French candidate node of the ESFRI project EuroBioImaging. In fact, the coordinator of the Institut Curie Cell & Tissue Imaging platform, Jean Salamero, is the national coordinator of France BioImaging and director of the UMS CEMIBIO (3714). This important support structure, created between Institut Curie and the CNRS, allows the national coordination of activities related to governance aspects, e-communi-cation and organization of platform access, technology transfer and training activities at both the national and international levels in all fields related to bioimaging.

Industry relations/Nikon Imaging Centre @ Institut Curie The platform has privileged relationships with industry, which often lead to joint developments through contractual platforms and gives research teams direct on-site access to new equipment prior to or as soon as it appears on the market. Strong partnerships have been established with Roper Scientific, based on joint developments and Nikon France and Euope B.V. Since 2007, the platform hosts and administers the Nikon Imaging Centre @ Institut Curie - CNRS (http://nimce.curie.fr/), one of only nine centres of this kind worldwide and the sole one in France.

Overall coordination Dr Jean Salamero (Team leader, UMR144)Dr Daniel Lévy (Team leader, UMR168)

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Biophenics is also part of the IBiSA labelled PICT platform structure

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Biological imaging is undergoing a permanent revolution since the early 90s. Gathering advanced equipment and expertise for excellent biomedicalresearch is our day to day challenge - guided by our mantra ‘Innovation-Training-Access’ - Jean Salamero

Characterization of morphogenesis during metamorphosis (Drosophila dorsal thorax); Credits: B Guirao,

S Rigaud, F Bosveld (U934/UMR3215)

Histology permits the characterization of healthy and diseased tissue at cellular and molecular level. It is essential in clinical research and particularly in the fight against cancer because it allows to analyse and understand morphological and biochemical modifications during cancer develop-ment and response to treatment.

The Histology platform provides dedicated equipment and technical support for histological projects to all research groups at Institut Curie. The facility treats animal or human tissues (xenografts), biopsies and cell pellets. Entire experiments, from sample preparation to staining, can be run by the platform or, alternatively, technical assistance and personalized training in histology techniques and protocols are provided. All embedding and sectioning materials for paraffin, agarose or cryo sections along with a paraffin distributor, microtomes, a vibratome, cryostats and microscopes are available. Most histological techniques require caution and rigor and the appropriate method (staining, in situ hybridization, immune-staining) is chosen together with the customer, depending on the nature of the study and the question asked.

Users have access to powerful computers dedicated to image analysis. Specialized commercial software (Metamorph, Amira, Huygens, Matlab, Imaris) as well as several innovative tools developed by the platform are available, e.g. for segmentation, tracking, deconvolution, denois-ing, colocalisation, image registration, etc. Development of image analysis and processing tools is another important part of the platform activity. Several ImageJ plugins for image quantification tools have been developed (e.g. object counting in 3D, endosomes and cell tracking, mobile part and background separation in movies, etc.), some are accessible through other open source software platforms (eC-CLEM under Icy) or are eventually integrated under the Metamorph software (e.g. denoising-nDSafir, wavelet- based segmentation).

Techniques • Monophoton and multiphoton point and multi-point scanning microscopy • High resolution photonic setup (FLIM-FRET, FAIM, TIRFM, PALM/dSTORM, SIM, multiangle TIRFM) with a focus on dynamic imaging of molecular processes at the single-cell level and in model organisms. • Active illumination (FRAP, Photo-Activation, Photo-Ablation, DNA damage) • Intra-vital imaging for longitudinal studies • Light-sheet based microscopy • Live CLEM (correlative light - electron microscopy) • Long-term live cell imaging on cells, tissues and embryos

Electron microscopy provides insight into molecular and cellular ultrastructure nanometer and sub-nanometer resolutions by cryo-methods including high pressure freezing, cryo-sectioning and immunolabeling for localization of molecules, cryo-electron microscopy and cryo-tomography.

The Electron Microscopy platform is under the responsibility of three teams with complementary expertise including cellular electron microscopy (G. Raposo), molecular cryo-electron microscopy (D. Lévy), 3D-electron microscopy and 2D and 3D chemical imaging (S. Marco). The equipment comprises three electron microscopes and several instruments for sample preparation such as cryostats and ultra-microtomes.

Techniques • Cellular 2D and 3D (tomography) electron microscopy of resin-embedded samples • Cellular sample preparation (resin embedding, immunolabelling, Tokuyasu) • CLEM (correlative light - electron microscopy) • 2D and 3D cryo-electron microscopy • 2D and 3D electron microscopy of negatively stained samples

Ultra-structural analysis of biological samples can be of great interest when combined with chemical mapping and spectroscopic analysis because it provides qualitative and semi-quantitative informa-tion on the distribution of chemical elements on a given sample. This can be approached by second-ary ion mass spectroscopy imaging, and by analytical transmission electron microscopy in scanning (Z-contrast) end energy loss modes (Electron Energy Filtered TEM or EFTEM and Electron energy loss spectroscopy or EELS). Combining the two latter modes with electron tomography for biological samples represents a technological challenge that the platform is approaching together with the correlation of SIMS data with chemical imaging in 2D and 3D (tomography) by analytical-TEM.

Techniques • nanoSIMS imaging • Cryo-fixation (slam and plunge freezing) / Freeze-drying / Ultramicrotomy • EFTEM (2D/3D) • STEM (2D/3D) • Cryo-tomography • RT-tomography • Consulting in image processing and analysis

HistologyElectron Microscopy (Paris & Orsay)

Chemical Imaging (Orsay)

ManagersDr Daniel Lévy (Team leader, UMR168)Dr Graça Raposo (Deputy director, UMR144)Dr Sergio Marco (Deputy director, UMR9187/U1196)

ManagersDr Sergio Marco (Deputy Director, UMR9187/U1196)Dr Jean-Luc Guerquin Kern, Dr Sylvain Trepout (UMR9187/U1196)

Manager Sophie Leboucher

In-house service:

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2-photon laser scanning confocal microscope

BioPhenics uses automated fluorescent microscopy imaging technology for phenotypic charac-terization of siRNAs and small-molecule effects on cellular systems for identifying both, the genes and pathways that mediate disease states, and novel compounds that modulate these pathways.Our mission is to enable basic and translational biomedical research by helping research teams to develop successful high content screening bioassays to be used in conjunction with their developed disease-relevant cell models. Insights from the phenotypic information-rich analyses allow to accelerate the discovery of biomarkers, as well as to understand pharmacological and toxic properties of bioactive chemical molecules at the early stages of discovery. The platform provides access to family-wide siRNAs collections, as well as chemical compound libraries. The effect of small molecules or knockdown of specific genes can then be evaluated with an unparalleled level of finesse using 96- and 384-well plates.With hands-on experience and comprehensive instrumentation, the platform serves both as an intellectual base and a service facility. It allows researchers to pursue their goals to discover gene functions and novel treatments for diseases, bringing to successful completion even the most challenging projects.

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Image-based high-content screening, biochemical and cell-based screening, phenotype tracking, siRNAs collection; chemical compound libraries

Yeast functional genomics, chemo-genomics, S. cerevisiae, systems biology, interaction networks

Services

Detecting interactions among different cellular components brings us closer to understanding their complex functions and helps to elucidate mechanisms of disease. An important contribu-tion in this context was made with the automated generation of yeast mutants in a high-through-put manner to uncover genetic interactions. Further on, this approach extended to reveal protein interactions, chemo- and toxico-genomic interactions and localization studies. Evolutionary conservation of core processes makes it possible to study them comparatively fast and cheap in the baker’s yeast Saccharomyces cerevisiae and to translate the findings to other cellular systems, for example human cells. The platform provides extensive collections of S.cerevisiae mutants including deletions of non-essential genes, perturbations of essential genes , BiFC collection for protein interaction on the basis of bimolecular fluorescence complementation and several other specialized collec-tions. In addition, the platform’s expertise and involvement in projects from experimental design to data analysis enables users to advance faster in their research.

Depending on the experimental set-up SGA allow to:• Study gene or protein functions and their interactions.• Elucidate the mechanism of action of drugs.• Construct fluorescently labelled yeast strain collections for high-content microscopy.

Services

• Agar based assays: - Chemical genomics or toxicogenomics - High-throughput construction of double or higher-order mutants• Liquid based assays to monitor growth in real time

• Computational analysis: - Quality control of experimental data - Identification of potential interactors - Gene ontology enrichment - Interaction networks

Mission and activity

Mission and activity

Manager Petra Kaferle

ManagerElaine Del Nery, Ph.D.

• Development of cell-based assays for large-scale identification of protein markers of a physio- logical or functional status of therapeutic response.• Drug sensitivity and resistance testing using FDA-approved-drugs or other investigational libraries. • Quantitative analysis of dose-response and drug combinations. • siRNA screening using family-wide siRNA libraries.

Affiliated with PICT-IBiSA overall platform

The platform provides basic and applied research teams with the intellectual base and expertise needed to carry out customized multi-parametric cellular imaging assays for discovery of novel biomarkers and bioactive compounds to fight cancer.

The significant evolutionary conservation of yeast genes allows to use yeastin functional studies of human disease, mechanisms of action of drugs or even off-target effects. At the SGA platform we provide the technology and expertise to take advantage of this.

20 21HIGH THROUGHPUT SCREENING HIGH THROUGHPUT SCREENING

Scientific advisors Dr Jacques Camonis (Team leader, ‘ Analysis of transduction pathways’, U830)Dr Franck Perez (Team leader ‘Dynamics of Intra-Cellular Organization’, UMR144)Dr Philippe Benaroch (Team leader ‘Intracellular Transport & Immunity’, U932)

Scientific advisor Dr Angela Taddei (Director, UMR3664 – Nuclear Dynamics)

Translational gateAffiliated with Translational Research Department (Head: Sergio Roman Roman)

Cytomat™ 6000K automated incubator

Mission and activity

Chemistry, chemical biology, small molecules, hit-to-lead optimisation Flow cytometry, cell sorting

Manager Dr Claire Beauvineau

Services• Compound collection available in various formats• Help with sample selection by molecular modelling and virtual screening• “hit-to-lead” expertise; synthesis of structural analogues• Molecular chemistry to identify the biological target

The Institut Curie/CNRS Chemical Library was created 65 years ago from chemical molecules synthesized by the institute’s chemists motivated by the discovery of molecules for cancer treatment. This academic chemical library is one of the most important ones in France and part of the French National Chemical library. It constitutes not only the final products, but also synthet-ic intermediates obtained during optimisation against various therapeutic targets. The Chemical Library continues to grow by addition of the new molecules synthesized by the chemists.Advances in proteomics and genomics have led to the discovery of an increasing number of new targets with therapeutic potential. Screening small molecules, either individually or as compound libraries, opens up opportunities to discover biologically active molecules, which are tools in “Chemical Biology” or “drugs of tomorrow”.

Mission and activityThe purpose of the flow cytometry platform is cell sorting, training and support for users on the self-service cytometers and related software, as well as advice on cell preparation and data acquisition and analysis.

Flow cytometry measures the fluorescence and light diffraction on large numbers of particles, i.e.cells, beads, bacteria, yeast, or organelles at speeds of up to 40,000 cells per second. Flow cytometry is used to simultaneously quantify multiple markers on cells, with the ability to sort up to 6 sub-populations of interest. The main advantage of flow cytometry is the speed of acquisition of data on large numbers of cells, allowing the analysis of complex and/or rare sub-populations with the possibility to sort and subsequently culture or analyse these pure populations using molecular biology tools. The cells in suspension can be simultaneously stained with up to 25 fluorochromes, each identifying a molecule of interest. The stained cells flow past multiple lasers and the fluorescence intensity is quantified cell by cell for each fluorochrome on thousands to millions of cells. Many fluorescent probes are availablento detect cellular functions such as membrane potential or pH changes, cell cycle (proliferation, apoptosis, doubling time), oxidation and calcium flux.

Currently the library contains over 10.000 compounds and is continually growing. Screening of the library has resultedto date in 10 patents and the creation of three start-ups.

The availability of a 5 laser, 21 parameters, 6 way sorting apparatus enclosed in a laminar flow cabinet allows the in-depth analysis of the tumour microenvironment at Institut Curie. - V. Soumelis

Services• Cell Sorting• Multiparametric high-speed analysers• Personalized user training (hands-on and theoretical)• Advice on cell preparation and choice of fluorochromes• Support for data acquisition and analysis• Software training for data acquisition and analysis

ParisManager Zofia Maciorowski

OrsayManager Charlène Lasgi

22 23HIGH THROUGHPUT SCREENING CYTOMETRY

Scientific advisors Dr Frédéric Schmidt (Team leader ‘Chemistry Of Biomolecules, Probes, and Heterocyclic Inhibitors, UMR3666/U1143) Dr Florence Mahuteau-Betzer (UMR9187 / U1196 – Chemistry, Modelling and Imaging For Biology)

Scientific advisors Paris Dr Olivier Lantz (Team Leader ‘Innate Like and Cd4+ T Cells In Cancer’, U932)Orsay Dr Jacques Ghysdael (Team Leader ‘Cellular Signaling and Oncogenesis’, UMR3348)

Molecular structures of biologically active small molecules

Experimental RadiotherapyPatient derived xenografts (PDX), pharmacology, biomarkers, drug resistance Experimental radiotherapy, radiobiology, proton therapy, ionizing radiation, radio-sensitivity,

patient derived xenografts, tumour models, preclinical trials

Manager Dr Didier Decaudin

Translational gateAffiliated with TranslationalResearch Department (Head: Sergio Roman Roman)

Manager Dr Frédéric Pouzoulet

Services

Mission and activity

Services

Cancer treatment is continuously evolving with many potential medications being developed. However, clinical trials are costly, time-consuming, and expose patients to side effects. Without prior preclinical evaluation the ethics and economics of conducting them would be questionable. Preclinical investigation of anti-tumour compounds on tumour models is an important step in the process of drug development. To obtain preclinical results with high predictive value for clinical trials, the choice of the preclinical tumour models is a crucial point.Human primary xenografts, directly obtained from cancer patients, constitute the main category of preclinical cancer models. They well reproduce the high heterogeneity of human cancers, procedures for assessment of therapeutic efficacy are well standardized and easily allow the evaluation of combined therapies, and the possibilities of ex vivo genetic or therapeutic manipula-tions before xenotransplantation are important.

The research performed at the Laboratory of Preclinical Investigation is an important complement to the screenings performed by pharmaceutical companies. The Laboratory of Preclinical Investigation is actively involved in molecular and experimental pharmacology and its activities create a space where clinicians can collaborate with biologists working on basic research questions and with partners from pharmaceutical companies. The platform is also a member of the European EuroPDX consortium which has the aim of sharing patient derived tumour xenografts for collaborative research projects and multicentre preclinical trials.

Mission and activityThe Experimental Radiotherapy platform brings together the scientific and technical expertise, ranging from medical physics to pre-clinical and clinical research, required for the development of new radiation therapy strategies.

The platform offers access to a large panel of irradiation systems, tools and skills, which, in the framework of preclinical and translational studies, allow to thoroughly investigate innovative radiotherapy techniques, such as combined treatments, complex irradiation configurations, higher dose rates, new radiation types. Available irradiation sources include Caesium 137 for cell and mouse whole body irradiation, and X-rays for mouse localized irradiations of xenografts or organs in toto and energy modulation experiments. A combined X-ray irradiator/CT imager enables ultra-localized, image-guided irradiations and dose distribution computation, allowing reproduction of real radiotherapy set-up techniques on animals. An electron linear accelerator provides unique ultra-high dose rate (up to 4000 Gy/s). Through a steering committee access to the proton beam lines of the Proton Therapy Centre (CPO) in Orsay is available, where a dedicat-ed experimental line and laboratory are being developed.

The platform is a member of the Resplandir network of French irradiation platforms, which in turn is part of the national infrastructure France Hadron.

To date the platform has developed over 300 PDX models for a variety of cancers – this includes the most comprehensive collection of breast cancer models world-wide with more than 100 models established and a unique model for uveal melanoma.

• Development, validation and maintenance of preclinical models and provide guidance to collaborators and the community.• Evaluation of anti-tumour effect of new compounds and new combinations of treatment and definition of optimal administration schedules.• Identification of biological markers of response and resistance to tested therapies and evalua- tion of their predictive value on other well characterized preclinical models.• Development of specific models such as orthotopic tumours, metastase-, clinically resistant- or circulating tumour cell-derived xenografts.• Evaluation of the efficacy of new therapies on metastatic localisations.

Significant advance has been made in radiation therapy techniques in the past years. Now the challenge is to apply them to cellular or small animal models and this is where the Experimental Radiotherapy platform comes in

24 25IN VIVO EXPERIMENTATION IN VIVO EXPERIMENTATION

Deputy manager Elisabetta Marangoni

• Support for project design, ensuring selection of appropriate radiation source.• Access to a whole suite of sophisticated irradiation systems.• Cone Beam Computed Tomography (CBCT) imaging for image-guided radiation therapy.• Characterization of radio-sensitivity of tumour models.• Acute/late radio-toxicity models (bone marrow aplasia, pulmonary fibrosis, heart failure, neuro toxicity, radio-induced carcinogenesis, etc.). • Animal experimentation: grafts, treatments, tumor growth follow-up, sampling, etc.

SARRP (Small animal radiation research platform)

Orthotopic PDX primary central nervous system lymphoma model.

Manager & Scientific director Dr Emmanuel Barillot, (Director, U900 – Bioinformatics, Biostatistics, Epidemiology and Computational Systems; Biology Of Cancer)

Deputy manager Dr Philippe Hupé(UMR144/U900)

In spite of substitutive methods, which are used wherever possible, the responsible use of small animal models, i.e. mouse, zebrafish, amphibian, remains required for research activity at Institut Curie. The care and use of animals at the institute is in strict compliance with the relevant European and national legislation for the protection of vertebrate animals used for experimental and other scientific purposes. Institut Curie fully adheres to the 3Rs principle: Replacement, Reduction, and Refinement of animals in research. The platform reports to the Ethics Committee of Institut Curie and activities are guided by the institute’s Animal Welfare Body. A team of 26 qualified animal technicians and engineers supervised by a platform manager and with assistance from a veterinarian provides daily support and services to more than 50 research groups and over 300 users.In addition to providing state-of-the-art breeding, housing and high welfare conditions for small animals, the platform offers a large panel of services and collaborative support, such as: • Technical support for protocols or equipment use. • Generation of genetically-engineered animal models (pronuclear DNA injection, homologous recombination in embryonic stem cells and CRISPR technology). • Mouse sperm and embryo cryopreservation and revitalization. • Animal import and export for external collaborations. The platform is constantly evolving through refurbishment and upgrade of the animal facilities and development and implementation of new services from extensive technology watch and collaborative benchmarking.

Institut Curie is part of numerous networks with the dual objective of high quality research and respect of animals such as EU-LIFE, AAALAC (Association for Assessment and Accreditation of Laboratory Animal Care), AFSTAL (Association Française des Sciences et Techniques de l’Animal de. Laboratoire), CELPHEDIA (Création, Elevage, PHenotypage, Distribution et Archivage d’organismes modèles), GIRCOR (Groupe Interprofessionnel de Réflexion et de Communication sur la Recherche).

The Bioinformatics platform offers multidisciplinary expertise to support the biotechnological platforms, the research units and the hospital in their daily activities. The skills range from statistical data analysis and data management to software development and high performance computing.This covers fundamental, translational and clinical research, as well as clinical routine and the platform frequently sets up collaborative projects with biologists, clinicians and others.The platform activities can be summarized in five key points: (1) Knowledge and data integration - setting up of a seamless information system for knowledge and data sharing, data query, visualization and analysis. (2) Collaborative support to biologists or clinicians for bioinformatics and biostatistics data analysis. (3) Advice and training in biostatistics and bioinformatics. (4) Support to high performance computing. (5) Coordination of bioinformatics activities within Institut Curie.

• Statistical analysis, in particular of omics and clinical data obtained from high-throughput technologies.• Development, maintenance and running of automatic bioinformatics pipelines, especially for biotechnological platform data processing, including quality control and first level analysis.• Support to the precision medicine program and delivery of decision-making reports in real-time for physicians.• Research and development for new biostatistical methods and bioinformatics tools.• Support to high performance computing.• Leveraging the high performance computing infrastructure with the use of big data technologies.

Services

Mission and activity

Mission and activity

The bioinformatics platform is strongly linked to the research units and platforms of the research centre and many departments of the hospitalwithin Institut Curie. We have developed many partnershipsin France, Europe and abroad and are involved in several key national and international initiatives

Data integration, statistical analysis, big data, high-performance computing,precision medicine, NGS data analysis, proteomics data analysis

26 27IN VIVO EXPERIMENTATION BIOINFORMATICSThe platform is part of the national genomics infrastructure France Génomique

8-cell stage compacted mouse embryo (Red;E-Cadherin Cyan;Actin), Images provided by JL Maître

The Pierre-Gilles de Gennes Institute (IPGG) gathers all microfluidics related research activities with the aim to develop both fundamental and applied research in this highly cross-disciplinary area by bringing together experts in physics, biology, chemistry, and technol-ogy. The IPGG is located on the Montagne Sainte-Geneviève campus in Paris, in close proxim-ity to Institut Curie, which is one of the IPGG partners along with ESPCI Paris, Chimie ParisTech and ENS.

The IPGG technology platform, in a unique set-up in Europe, assembles all the technologies and tools necessary for the realization of microfluidic devices, which allows users to fully achieve a microfluidic chip in a minimum of time from conception until its fabrication and characterization.

• Prototyping to rapidly test microfluidic chip designs• Photolithography to create channel micro-patterns• Micromachining to manufacture microstructures on metal plates or polymers• Chip fabrication (PDMS, NOA, COC)• Imaging platform to observe biological material and flow in chips• Various equipment to characterize microfluidic chips• Thin metal layer deposition (e.g. for integrating electrodes, etc.)• Theoretical and practical training in a dedicated laboratory equipped with microscopes and flow control systems.

Services

Mission and activity

28 ASSOCIATED PLATFORM www.institut-pgg.fr

Stefania Lemmi©

26 rue d’Ulm, 75248 Paris Cedex 05 FranceTel +33 (0)1 56 24 55 00www.institut-curie.org

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Institut Curie is a founder member of Paris Sciences et Lettres PSL Research University

A private charitable foundation since 1921

The information given in this publication is correct at the time of going to press. Nov. 2016

Alterations may occur to the services described in this brochure. For the most up-to-date information and more details on equipment, access policies, pricing, etc.

please visit the website www.science.institut-curie.org/platforms

Contact DetailsDr Andrea Hutterer

Tel: +33 (0) 1 56 24 64 55andrea.hutterer@curie.fr

CurieCoreTech: At the core of your activities

Photos unless otherwise stated: Uriel Chantraine/Institut Curie