systems pathology: an introduction to omic approaches in...
TRANSCRIPT
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Systems Pathology: An Introduction to Omic
Approaches in Personalized Medicine
Michael H. A. Roehrl, M.D., Ph.D.
Department of Pathology and Laboratory Medicine
Boston Medical Center
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This session will introduce practicing pathologists, pathologists in training, and
laboratory professionals to the concepts of
• the basics of cutting-edge Omic technologies,
• the basics of genomics, transcriptomics, proteomics, and metabolomics,
• next generation DNA and transcriptome sequencing,
Our Goals for this Course
• next generation DNA and transcriptome sequencing,
• the significance of cancer genome alterations for personalized treatment
decision making,
• mass spectrometry as an up and coming exciting enabling technology to look at
proteomes of diseased tissues, and
• the pathologist's key role in optimal large-scale biospecimen banking for
molecular pathology and research.
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Examples will be included how to beneficially integrate novel Omic diagnostic
workflows into existing and future pathology workflows.
This course will equip participants with key tools for practicing pathology in the
future.
Our Goals for this Course
Don’t worry: No prior knowledge of molecular pathology is assumed.
We’ll cover the basics and equip you with the skills to evaluate, communicate, and
understand future trends in personalized pathology diagnostics.
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This is a brand new course!
So please enjoy and ask lots of questions!
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What do I have?
Why did I get it?
How will it behave?
Diagnostic
Etiologic
Predictive
The Fundamental Questions
How will it behave?
How will it respond?
Predictive
Therapeutic
Need to understand personalized pathophysiology.
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Current Challenges in Cancer Diagnostics
• Diagnosis largely based on morphologic characteristics
• Limited number of diagnostic biomarkers
• Lack of prognostic and predictive markers• Lack of prognostic and predictive markers
• Lack of global personalized picture of molecular aberrations
• Difficulty to interpret tumor heterogeneity and tumor-stroma interplay
• Difficulty to extrapolate to individualized treatment recommendations
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What is Omics?
• The suffix –ome (as used in molecular biology) refers to a totality of some sort
• Early uses: Biome (1916) and Genome (1920)
• Most common uses today: Genome, Transcriptome, Proteome, Metabolome
• “Explosion” of uses: Connectome, Cytome, Exposome, Exome, Glycome, Interferome,
Interactome, Ionome, Kinome, Lipidome, Mechanome, Membranome, Metagenome,
Metallome, ORFeome, Organome, Pharmacogenome, Phenome, Physiome, Regulome,
Secretome, etc.
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What is Omics?
• Genomics: Global study of genomes of organisms; determination of the entire DNA
sequence; fine-scale genetic mapping; first DNA genome (bacteriophage) in 1977 (F.
Sanger); first free-living organism (H. influenzae) in 1995; Human Genome Project
(draft, 2001; “finished”, 2007, <1 error per 20,000 bases); technologies: classical
sequencing (Sanger), “next generation” DNA sequencing
• Transcriptomics: Global study of all RNA molecules (mRNA, rRNA, tRNA, other non-
coding RNA) in a cell or tissue type; quantification, distribution, time-dynamic coding RNA) in a cell or tissue type; quantification, distribution, time-dynamic
plasticity; technologies: RT-PCR, nucleotide arrays, “next generation” RNA-Seq
• Proteomics: Global study of all proteins in a cell or tissue type; quantification,
distribution, time-dynamic plasticity, chemical modification (phosphorylation,
methylation, glycosylation, etc.); term first introduced in 1994 (Marc Wilkins);
technologies: gel-based systems, antibody arrays, mass spectrometry
• Metabolomics: Global study of all “small molecules” in a cell or tissue type;
quantification, distribution, time-dynamic plasticity, chemical composition;
technologies: chromatography, mass spectrometry, NMR spectroscopy
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The Link: Omics and Systems Biology
• Systems Biology: Comprehensive integration of genomic, transcriptomic, proteomic,
and metabolomic data to give a (more) complete picture of a cell/tissue/living organism
(this remains an unsolved problem and is an area of very active research)
• Systems Pathology: Application of Systems Biology concepts and tools to the study and • Systems Pathology: Application of Systems Biology concepts and tools to the study and
diagnosis of disease; key scientific concept for Personalized Disease Management
(outstanding opportunity for Pathology to take center stage in Molecular Medicine!)
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source
RNA
Proteins
Metabolites
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology
RNA
Proteins
Metabolites
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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Currently
Morphology Classification of diseases
DiagnosisStatic assessment
Specimen
Treatment
Assessment of response
(predominantly by imaging)
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Functional assessment
Specimen
Morphologic assessment
Diagnosis
Classification of diseases
Pathophysiologic-dynamic assessment• Spatial heterogeneity (stem cells etc.)
• Omic parameters (WGS, transcriptome, proteome,
metabolome)
• Dynamic behavior
• Functional treatment response
TreatmentContinuous functional treatment
response monitoring
• Functional treatment response
Therapy adjustment
...
Transformative
Pathology
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Genomics
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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First Generation Sequencing
Conventional Sanger
sequencing workflow
Roehrl et al., 1996
Shendure, Li. Nat Biotech, 2008
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Next Generation Sequencing
Conventional Sanger
sequencing workflow
Next gen sequencing
workflow
Shendure, Li. Nat Biotech, 2008
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Next Generation Sequencing
Applications
• De novo sequencing of whole genomes
• Resequencing (genome variations, mutations, etc.)
• “Tag counting” (gene expression, chromatin occupancy, ChIP-Seq, methylation
analysis) by short identifiable tag sequencing
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Next Generation Technologies
Kahvejian et al. Nat Biotech, 2008
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Next Generation Technologies
Kahvejian et al. Nat Biotech, 2008
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Next Generation Technologies
Kahvejian et al. Nat Biotech, 2008
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Next Generation Sequencing
• Dideoxy sequencing (Sanger method)
• Solid phase sequencing
• Sequencing by hybridization
• Mass spectrometry
• Cyclic array sequencing
• Nanopore sequencing
• Other emerging platforms
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Next Generation Sequencing
Clonal amplification strategies
Emulsion PCR
(454, Polonator,
SOLiD)
Shendure, Li. Nat Biotech, 2008
Bridge/Cluster
PCR
(Solexa/Illumina)
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Next Generation Sequencing
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Next Generation Sequencing
454
Illumina/Solexa
Platform
Shendure, Li. Nat Biotech, 2008
SOLiD, Polonator
HeliScope
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Next Generation Sequencing
Non-Fluorescence Methods (Ion Torrent)
Life Technologies Corp.
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Next Generation Sequencing
Example workflow for Illumina sequencing
Target selection:
Whole genome
Exome
RNA
Custom
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Next Generation Sequencing – Sequence Assembly
Sequence assembly from NGS reads (from data to finished sequence)
• Many algorithms available
• Under very active investigation
• De novo assembly: No reference genome required
• Mapping-based assembly: Uses a reference genome for assembly• Mapping-based assembly: Uses a reference genome for assembly
How does it work (in principle)?
Reference genome
Mapping algorithm
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Next Generation Sequencing – De Novo Assembly
Overlap graph approach
De Bruijn graph approach
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Next Generation Sequencing – De Novo Assembly
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Next Generation Sequencing
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Exome Enrichment
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Exome Enrichment
• ~30,000 targets (36.5 Mb)
• From various databases (ResSeq, CCDS,
miRBase)
• 2.1 million oligonucleotide probes
(covering 44.1 Mb)
Roche NimbleGen, Inc.
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Cancer Genomics: Workflow
Myerson et al. Nat Rev Genetics, 2010
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Cancer Genomics: Next Generation Sequencing
Myerson et al. Nat Rev Genetics, 2010
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Cancer Genomics: Recent Examples
Myerson et al. Nat Rev Genetics, 2010
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Cancer Genome Projects
• The Cancer Genome Atlas (TCGA) – comprehensive analysis of 20-
25 tumor types; data available on glioblastoma and serous ovarian
cancers
• The International Cancer Genome Consortium (ICGC) – large-scale
international cancer genome sequencing effort (50 tumor types)
• The Pediatric Cancer Genome Project (PCGP) – cancer genome
sequencing of 600 childhood cancer patients
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Next Generation Sequencing – Why Did It Develop Just Now?
• Next gen sequencing (thus far mostly) borrows from original Sanger sequencing principles
(chain termination, sequencing by synthesis)
• Improvements in cyclic in-situ chemistry (polymerase, modified nucleotides, reversible
blocking moieties)
• Massive parallelization in space and time (by using 2-D immobilization or nanowells)
• Improvements in fluorescence chemistry
• Breakthroughs in nanofabrication and microfluidics
• Breakthroughs in high-resolution digital imaging
• Breakthroughs in high-performance computing, data storage, and analysis algorithms
(under very active development, “cloud” outsourcing)
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Medical Impact of Exome Sequencing – An Example
June 11, 2011
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Medical Impact of Exome Sequencing – An Example
Let’s look at the Methods section – now it is much clearer!!!
shotgun library
in-solution exome capture
Tiacci et al. NEJM, 2011
next gen sequencing
?
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Medical Impact of Exome Sequencing – An Example
Bioinformatics workflow
is key but not trivial!
Tiacci et al. NEJM, 2011
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Next Generation Sequencing – A “Software Zoo”
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Medical Impact of Exome Sequencing – An Example
• The genomic basis of Hairy Cell Leukemia (HCL) was unknown
• Next gen exome sequencing of leukemic and normal cells from ONE (!) index patient
• Identification of 5 somatic mutations (including BRAF V600E)
• BRAF V600E found in 47 other HCL patients (100% of tested patients) by targeted Sanger
sequencingsequencing
• No BRAF V600E found in 195 patients with other leukemias/lymphomas by targeted
Sanger sequencing
• Functional demonstration of MEK and ERK phosphorylation as downstream targets of
BRAF activation
• BRAF inhibition reduces phosphorylation of MEK and ERK
Tiacci et al. NEJM, 2011
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Next Gen Sequencing – Open Questions
• Ethics and informed consent (GINA etc.)
• Next gen technologies in a CLIA setting (proficiency testing, QC, etc.)
• Who will perform the testing clinically and who will interpret the data? (Pathology!)
• How define “clinically actionable” mutations (e.g., if a clinical trial is not available for the
target)?
• Billing for Omic Testing?
Today: Fragmented billing, even for simple molecular tests... Tomorrow: Hopefully, task-based billing!
• Exome analysis for solid tumors
• Transcriptome analysis
• Proteome analysis (phosphorylation state)
• ...
• Pathologist’s data interpretation as key
billable component!
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Transcriptomics
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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Transcriptomics: DNA Arrays
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Transcriptomics: DNA Arrays
Disadvantages of array-based transcriptomics:
• Limited linearity and dynamic range (no “digital” read-out as in NGS)
•No allele-specific read-out
•No discovery of alternative splicing or RNA editing•No discovery of alternative splicing or RNA editing
• Cross-hybridization noise
• Interrogation limited by immobilized probe population
•Hard to scale and parallelize (no sequence bar-coding as in NGS)
Forecast: DNA arrays will likely be (largely) replaced by sequencing technologies
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
Wang et al. Nat Rev Genetics, 2009
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
Example:
Discovery of gene fusions in prostate
and gastric cancers involving the RAF
kinase pathway by paired-end RNA-
Seq
Palanisamy et al. Nat Med, 2010
FISH verification
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5 min break!
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Proteomics
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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3.2 ×××× 109 base pairs (haploid genome), 1.5% of which is the coding exome
Only ~20,500 protein-coding genes…
[+ non-coding ribonucleic acids and “ribozymes” (mostly ribosome)]
Diversity:
Why Study Proteins: Biologic Complexity in the Protein World
Diversity:
Polymorphisms (maybe 2××××)
Splice variants (maybe 3××××)
Post-translational modifications (phosphorylation, glycosylation,
transamination, alkylation, oxidation, etc.; maybe 3××××)
but ~400,000+ “different” proteins (!)…
and large dynamic complexity (~1012 – 1015)
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Mass Spectrometry in Pathology
• Mass spectrometry (MS) is an analytical technology that measures mass-to-charge
ratios (“m/z “) of charged particles.
• MS is used to elucidate and quantify chemical compounds, including peptides,
carbohydrates, metabolites, and other chemical entities
• A typical MS procedure consists of multiple steps:
• Sample is loaded onto the instrument and is vaporized• Sample is loaded onto the instrument and is vaporized
• Sample is ionized (charged)
• Ions are separated by m/z ratios in electromagnetic fields
• Ions are detected quantitatively
• Ion signals are processed into mass spectra
• MS instruments have 3 components:
• Ion source (to convert gas phase sample into ions)
• Mass analyzer (electromagentic fields)
• Detector
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
• Different sample sources:
• Solid (MALDI, laser ionization)
• Liquid (chromatographic separation, electrospray ionization)
• Different ways of handling ions:
• Quadrupole
• Ion trap (linear, 3-D)
• Different types of ion fragmentation:• Different types of ion fragmentation:
• ETD
• PTR
• CID
• ECD
• Popular instruments in the life sciences:
• Time-of-flight
• Triple quadrupole (good quantification, fast)
• Ion trap
• Variations thereof (e.g., qTOF)
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
Multiple Reaction Monitoring (MRM)
Pisitkun T et al. Physiology 2007;22:390-400
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Mass Spectrometry in Pathology
• In Laboratory Medicine:
• Vitamin D (superior to immunoassays)
• Steroid hormones
• Drug metabolites
• Immunosuppressant monitoring
• Biomarker discovery (blood, serum, plasma, urine, CSF, etc.) – research use• Biomarker discovery (blood, serum, plasma, urine, CSF, etc.) – research use
• In Anatomic Pathology (mostly research use):
• Biomarker discovery (tissues)
• MS imaging (“MALDI imaging”)
• Drug penetration
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Mass Spectrometry in Pathology
Pisitkun T et al. Physiology 2007;22:390-400
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Mass Spectrometry in Pathology
Pisitkun T et al. Physiology 2007;22:390-400
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Mass Spectrometry in Pathology
Predictable fragmentation patterns are key for identification!
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Mass Spectrometry in Pathology
Pisitkun T et al. Physiology 2007;22:390-400
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
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Mass Spectrometry in Pathology
1. Protein ID & PTM
2. TMT Quantitation
Easy nLC1000
Velos Pro
Nanospray Flex
Sample Preparation
Data Interpretation
REAGENTS & CONSUMABLES
Lysate Preparation
Protein Enrichment
Protein Clean-up
Protein Digestion
Peptide Enrichment
3. Absolute Quantitation
4. Glycan Analysis
SOFTWARE
Proteome Discoverer 1.3
Pinpoint 1.2
SimGlycan 2
Thermo Fisher Scientific
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Mass Spectrometry in Pathology
MALDI Imaging
(“Histology by MS”)
Schwamborn and Caprioli. Nat Rev Cancer, 2010
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Mass Spectrometry in Pathology
MALDI Imaging
(“Histology by MS”)
Schwamborn and Caprioli. Nat Rev Cancer, 2010
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Mass Spectrometry in Pathology
MALDI Imaging
(“Histology by MS”)
Schwamborn and Caprioli. Nat Rev Cancer, 2010
Drug distribution
within a tumor
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IEF & SDS-PAGE
:
Proteomic Analysis of Surgical Tissue
Tandem-MS/MS
Roehrl et al.
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Proteomic Analysis of Colon Adenocarcinoma
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Proteomic Analysis of Colon Adenocarcinoma
32/56 differentially regulated proteins (57%) were only discoverable after heparin enrichment.
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Tandem Mass Spectrometry of Differentially Expressed Proteins
2-D Gel Spot
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Tandem Mass Spectrometry of Differentially Expressed Proteins
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×2.5 ×5.2 ×9.3 ×37.02-D Western
Differential Regulation of PRDX1 Protein Isoforms
1-D Western ×22.2
2-D Western captures isoform differences!
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Tumor tissue is heterogeneous…
• Malignant cells
• Stroma
• Benign epithelial elements
• Inflammatory cells
• Blood and lymphatic vessels
• Nerve tissue
• Muscle• Muscle
• Extracellular matrix
Where is PSB7 up-regulated?
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PSB7 Up-Regulation in Colon Cancer
Lymphatics
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PSB7 Up-Regulation in Colon Cancer
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Functional Significance of PSB7 – MHC Class I Escape?
↑↑↑↑ IFN-γ
α7β7β7α7 ↓↓↓↓ PSB7
↓↓↓↓ IFN-γ
Conventional proteasome Immunoproteasome
↑↑↑↑ PSB7
↑↑↑↑ MHC presentation↓↓↓↓ MHC presentation
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Proteomic Alterations in Lung Cancer
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Transgelin Cell motility?
Proteomic Alterations in Lung Cancer
Transgelin-2
PPIA
Cell motility?
Isomerase
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Proteomic Alterations in Lung Cancer
TransgelinStroma
Transgelin-2 Carcinoma
“Spatial Mirror Images”
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Transgelin
Transgelin-2
Proteomic Alterations in Lung Cancer
65% identical
87% similar !Needleman-Wunsch protein sequence alignment
Yet very different pattern of
overexpression!
Transgelin Transgelin-2
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Transgelin
Proteomic Alterations in Lung Cancer
Transgelin-2
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Metabolomics
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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Mass spectrometry/NMR spectroscopy
Direct tissue extracts (soluble fraction,
membrane-bound, etc.)
Cancer Metabolomics
membrane-bound, etc.)
Metabolic ex vivo labeling (“bioreactor”)
using stable isotopes (13C glucose, 13C
amino acids, deuterated compounds, etc.)
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Tissue Extracts (Aqueous,
Organic)NMR Spectra (1D-ND)
Pulse Sequences
B
y
z
NMR Signal
Coil
Principles of NMR-Based Tissue Metabolomics
NMR Spectrometer Resonance Assignment
Statistical Methods
(Principal Component
Analysis, etc.)
Biomarker Discovery
xy NMR Signal
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NMR Pulse Sequences
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m = -1/2
Bo
Precessional
orbit around
applied
magnetic
fieldSpinning
Nucleus
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Relative
Energy
Bo
Bo
m = -1/2
I=1/2
Increasing Magnetic
Field Strength
o
m = +1/2
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Cancer
Normal
The 1H NMR Spectrum Reveals Metabolic Signatures
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Organic solvent
NMR
Aqueous solvent
LC-MS
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Chemical shift
range (ppm)
Average
cancer/normalAssignment Student t test
2.64..2.62 1.45 aspartate 0.00176
2.84..2.78 1.68 aspartate 0.000148
3.04..3.00 0.71 creatine 0.000193
3.92..3.90 0.69 creatine/glucose 0.000204
5.18..5.16 0.16 GlcNAc 0.00715
4.64..4.62 0.12 glucose 5.07E-06
5.24..5.20 0.2 glucose 3.36E-05
3.50..3.44 0.38 glucose 2.35E-06
3.72..3.70 0.62 glucose 0.00031
3.84..3.82 0.64 glucose 0.00307
3.90..3.86 0.66 glucose 0.000362
2.38..2.32 1.46 glutamate/proline 1.85E-06
8.18..8.16 1.62 IMP 1.04E-05
Normalized metabolite NMR peaks in aqueous spectra differing
significantly to at least 99% confidence between normal and cancer
tissue
8.18..8.16 1.62 IMP 1.04E-05
4.50..4.48 1.79 IMP 0.00369
4.38..4.34 1.96 IMP 0.000517
6.12..6.10 2.25 IMP 4.00E-05
1.38..1.28 1.22 lactate 0.00144
4.12..4.06 1.26 lactate/proline 0.00117
3.54..3.50 0.55 myo-inositol 1.53E-13
4.06..4.04 0.58 myo-inositol 1.79E-05
3.64..3.58 0.6 myo-inositol 4.13E-10
4.02..3.98 1.58 O-phosphoethanolamine 0.00209
2.56..2.50 1.51 oxidized glutathione 0.000942
3.34..3.32 0.64 scyllo-inositol 0.0038
3.26..3.22 1.59 taurine 2.42E-08
3.44..3.40 2.23 taurine/proline 6.44E-09
6.00..5.92 1.65 UDP-GlcNAc 0.00424
7.96..7.92 1.99 UDP-GlcNAc 2.23E-05
5.52..5.48 2.23 UDP-GlcNAc 0.00245
4.26..4.18 2.51 UDP-GlcNAc 0.000127
5.80. 5.78 2.02 uracil 0.000247
7.52..7.50 3.24 uracil 5.83E-07
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Cancer Normal
Unraveling Biomarkers By Principal Component Analysis (PCA)
Component
Co
mp
on
en
t
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Principal Component Analysis
Center at mean
Empirical covariance matrix
Eigenvector and eigenvalue decomposition
Principal components
Eigenvector Eigenvalue
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PC 1 vs. PC 2 plots for Pareto-
scaled and auto-scaled NMR
data. Borders were
constructed to optimally
separate between normal and
cancer.
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Hierarchical clustering of aqueous samples sorted by PLS-DA
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Biospecimen Banking
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The Art and Science of Biospecimen Banking
A Key Topic for the Future of PathologyA Key Topic for the Future of Pathology
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What do I have?
Why did I get it?
How will it behave?
Diagnostic
Etiologic
Prognostic
The Fundamental Questions
How will it behave?
How will it respond?
Prognostic
Predictive
Need to understand personalized pathophysiology
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Current Challenges in Cancer Diagnostics
• Diagnosis largely based on morphologic characteristics
• Limited number of diagnostic biomarkers
• Lack of prognostic and predictive markers• Lack of prognostic and predictive markers
• Lack of global personalized picture of molecular aberrations
• Difficulty to interpret tumor heterogeneity and tumor-stroma interplay
• Difficulty to extrapolate to individualized treatment recommendations
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1. The Central Role of Pathology in BioBanking
2. BioBanking Challenges
BioBanking in Pathology: Outline
3. Ultra-Rapid BioBanking at Boston Medical Center
4. Examples: Scientific Applications from My Lab
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Pathology Takes
Center Stage
Transformative Pathology and Biospecimen Science
at Boston Medical Center
Diagnostics
Biospecimens
Center Stage
Pathology meets with the patient and
owns the informed consent process (>95%
consent rate)
Basic Biomedical Research
BankingBioinformatics and
Database Structures
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Boston Medical Center BioBank Brochure for Patients
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Boston Medical Center BioBank Brochure for Patients
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1. The Central Role of Pathology in BioBanking
2. BioBanking Challenges
BioBanking in Pathology: Outline
3. Ultra-Rapid BioBanking at Boston Medical Center
4. Examples: Scientific Applications from my Lab
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BioBanking Legal Framework: HIPAA, GINA, CLIA
CLIA: Clinical Laboratory Improvement Amendments;
clinical laboratory performance standards
HIPAA: Health Insurance Portability and Accountability Act; HIPAA: Health Insurance Portability and Accountability Act;
defines protected health information (privacy); does
not explicitly cover privacy of genetic information
GINA: Genetic Information Nondiscrimination Act; privacy
of genetic information
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Patient Consenting at Boston Medical Center: The Pathologist’s Job!
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Patient Consenting at Boston Medical Center: The Pathologist’s Job!
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Frequently Overlooked Issues in Biospecimen Science
Ethnic diversity: Are discovered biomarkers sensitive to ethnic
background; most current BioBanks are biased in their assets!
Specimen annotation: Co-morbidities, drug treatments,
surgical procedure specifics, anesthesia, intraoperative
complications/delays, clamp times, etc.
Future-proofing of the collection: Does the current workflow Future-proofing of the collection: Does the current workflow
allow for scientific investigation using technologies not
envisioned at the time of collection (example: chemical
additives as preservatives may invalidate metabolomic
workflow)
Integration of tissue and biofluid collection: How good is the
longitudinal follow-up protocol, IT infrastructure, collaboration
between Anatomic Pathology and Laboratory Medicine
Comparability across sites: How standardized are collection
and storage protocols aross various sites
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African AmericanCaucasian
Ethnic Diversity in BioBanking: Key for Biomarker Discovery
Hispanic
Asian and other
Boston Medical Center BioBank
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Academic BioBanking: Succeeding in Times of Tight Funding
Academic Medical Center
Public funding for BioBanks
NIH, states
Academic Medical Center
Medical School
• High-complexity cases
• High volume
• Excellent clinical annotation
• IT infrastructure (EMR, BioBank)
• Active clinical trial site
Philanthropy for BioBanks
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Academic Medical Center
Public funding for BioBanks
NIH, states
Collaborative Agreements
with Biotech/Pharma
Academic BioBanking: Succeeding in Times of Tight Funding
Academic Medical Center
Medical School
• High-complexity cases
• High volume
• Excellent clinical annotation
• IT infrastructure (EMR, BioBank)
• Active clinical trial site
Philanthropy for BioBanks
Codevelopment of biomarkers
Clinical trials
Infrastructure funding
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1. The Central Role of Pathology in BioBanking
2. BioBanking Challenges
BioBanking in Pathology: Outline
3. Ultra-Rapid BioBanking at Boston Medical Center
4. Examples: Scientific Applications from my Lab
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Why Ultra-Rapid BioBanking?
What Does It Take to Do It?
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Tissue in FFPE Blocks: Harsh Chemical Exposure Limits Scientific Use!
Getting fixed tissue into paraffin
Dehydration (ethanol series)
Clearing (xylene)
Infiltration (molten paraffin)
Loss of:
Small molecules
Lipids
Peptides
Small RNAsInfiltration (molten paraffin)
Small RNAs
...
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
ProteomicsTissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
ProteomicsTissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
ProteomicsTissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
Proteomics
Tissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
ProteomicsTissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Science Platforms Drive Tissue Biospecimen Requirements
Formalin-fixed, paraffin-embedded (FFPE)
Tissue in “OCT”
(optimal cutting temperature; glycols/resins)
Genomics
Transcriptomics
ProteomicsTissue in some sort of “stabilizer”
(fixatives and/or degradation inhibitors;
e.g., RNAlater is ammonium sulfate)
Tissue at low temperature (LN)
Ultra-rapid procurement and low temperature
Proteomics
Proteomics with PTMs
Metabolomics
Lipidomics/Glycomics
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Integrated BioBanking Workflow at Boston Medical Center
Pre-OP visit
Clinical consenting
Pre-OP visit
BioBank consenting
(Pathology!)
IT Infrastructure (customized Freezerworks platform)
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Integrated BioBanking Workflow at Boston Medical Center
Operating RoomPre-OP visit
Clinical consenting
Pre-OP testing
Intraoperative Pathology Consult
(margins, diagnosis, molecular studies)
Operating RoomPre-OP visit
BioBank consenting
(Pathology!)
Pre-OP testing
Pre-OP BioBanking
(blood, urine, etc.)
Ultrarapid BioBanking
(tissue)
IT Infrastructure (customized Freezerworks platform)
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Integrated BioBanking Workflow at Boston Medical Center
Operating RoomPre-OP visit
Clinical consenting
Pre-OP testing
Intraoperative Pathology Consult
(margins, diagnosis, molecular studies)
Post-OP hospital stay Outpatient follow-up
Clinic visits
Operating RoomPre-OP visit
BioBank consenting
(Pathology!)
Pre-OP testing
Pre-OP BioBanking
(blood, urine, etc.)
Ultrarapid BioBanking
(tissue)
Post-OP hospital stay
Post-OP BioBanking
(blood, urine, etc.)
Outpatient follow-up
Follow-up BioBanking
(re-biopsies, blood, urine, etc.)
IT Infrastructure (customized Freezerworks platform)
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Consultation Ultra-Fast BioBanking
Intraoperative Pathology Consultation:
The Gateway To High-Quality Tissue Proteomics
0 min
1 min
<5 min5 min
10 min
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0 min
1 min
Intraoperative Pathology Consultation:
The Gateway To High-Quality Tissue Proteomics
- Intraoperative Pathology (“Frozen Section Pathology”) provides high-value, real-time
diagnostic decision making information during surgery or other interventional procedures
(e.g., image-guided biopsies) and is a springboard for moving the future of pathology
forward
- Essential for BioBanking (speed of sample procurement, quality of material, achieving
highest banking rates)
5 min
10 min
highest banking rates)
- Critical for the future of molecular diagnostic medicine (functional assay development,
triaging, real-time assay development – genomic/transcriptomic/proteomic etc., therapy
response prediction and monitoring)
- Critical for patient care (real-time feedback)
- Critical for real-time personalized therapeutic/diagnostic decision making within the health
care team (pathologists, surgeons, medical oncologists, radiation oncologists)
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Logistics for Ultra-Rapid BioBanking
Frozen Section Laboratory
(Pathology)
Operating Room
Active communication
(rapid alert system)
BioBank
LN freezing
Barcoding
Initial database annotation
Intra-OR freezing
Pre-resection biopsy
Clinical Laboratory
(blood, serum, plasma, urine, CSF, etc.)
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Logistics for Ultra-Rapid BioBanking
Frozen Section Laboratory
(Pathology)
Operating Room
Active communication
(rapid alert system)
BioBank
LN freezing
Barcoding
Initial database annotation
Intra-OR freezing
Pre-resection biopsy
Clinical Laboratory
(blood, serum, plasma, urine, CSF, etc.)
Close time monitoring
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Logistics for Ultra-Rapid BioBanking
1. Establish rapid communication between OR, Pathology, and BioBank
2. Establish Intraoperative Pathology Consultation as a focus point2. Establish Intraoperative Pathology Consultation as a focus point
3. Collaborate with a good pathologist!
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Pathology Takes
Center Stage
Transformative Pathology and Biospecimen Science
at Boston Medical Center
Diagnostics
Biospecimens
Center Stage
Pathology meets with the patient and
owns the informed consent process (>95%
consent rate)
Basic Biomedical Research
BankingBioinformatics and
Database Structures
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Logistics for Ultra-Rapid BioBanking
1. Establish rapid communication between OR, Pathology, and BioBank
2. Establish Intraoperative Pathology Consultation as a focus point2. Establish Intraoperative Pathology Consultation as a focus point
3. Collaborate with a good pathologist!
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Logistics for Ultra-Rapid BioBanking
Frozen Section Laboratory
(Pathology)
Operating Room
Active communication
(rapid alert system)
BioBank
LN freezing
Barcoding
Initial database annotation
Intra-OR freezing
Pre-resection biopsy
Clinical Laboratory
(blood, serum, plasma, urine, CSF, etc.)
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5 min break!
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Systems PathologyMaking Diagnostic Medicine Quantitative and PredictiveMaking Diagnostic Medicine Quantitative and Predictive
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DNA mRNA Proteins
Metabolites
Substrates
Life
RNA Biosynthesis
Normal Disease
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What is Systems Pathology?
• Study of the interactions between the components of a biological
system (e.g., enzymes and metabolites)
• How these interactions give rise to the function and behavior of that • How these interactions give rise to the function and behavior of that
system
• Quantitatively describe biological processes
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Bands on a gel?Pathway pictorials?
Really Not Good Enough!(No offense, all data shown here by Roehrl et al.)
What is Systems Pathology?
More bands on a gel? Fluorescence tracking?
Even more bands on a gel?
(No offense, all data shown here by Roehrl et al.)
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Also Not Good Enough!
What is Systems Pathology?
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TheoryComputer
Modeling
What is Systems Biology?
Experiment
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What is Systems Biology?
TheoryComputer
Modeling
ExperimentGenomics
Transcriptomics
Proteomics Metabolomics
Physiomics
Glycomics
Interactomics
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130K Processors
280 TFlops
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130K Processors
280 TFlops
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Approaches to Modeling
• Quantum Mechanics (1-10 × 10-10 m)
• Newtonian Molecular Dynamics (10-500 × 10-10 m)
• Spatial (1-3 D) Convection, Diffusion, and Active Transport
• Chemical Kinetics (kon, koff, kcat, etc.)
• Deterministic (N Large) vs. Stochastic (N Small) Simulation
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Scaled Approaches to Modeling
0.1 nm 10 nm 1 µµµµm 1 mm 1 m0.1 nm 10 nm 1 µµµµm 1 mm 1 m
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0.1 nm 10 nm 1 µµµµm 1 mm 1 m
Scaled Approaches to Modeling
0.1 nm 10 nm 1 µµµµm 1 mm 1 m
Mesobiology
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Systems Biology: Quantitative Modeling
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Systems Biology: Quantitative Modeling
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Monte Carlo Stochastic Simulation
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Monte Carlo Stochastic Simulation
This is somewhat analogous to the Heisenberg uncertainty principle of QM…
Nanofluidics will have to deal with this to be
useful in the clinical lab of the future!
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0.1 nm 10 nm 1 µµµµm 1 mm 1 m
At What Scale Does Stochastic Behavior Live?
0.1 nm 10 nm 1 µµµµm 1 mm 1 m
Mesobiology
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Systems Pathology of Signaling: Modeling a Complex Network
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77 differential equations
112 rate constants
76 species
Modeling a Complex Network: Blood Coagulation
22 fluid phase factors
10 fluid phase complexes
19 lipid-bound factors
25 lipid-bound complexes
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Model Validation
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Thrombin (M)
3e-8
4e-8
Normal
Hemophilia A (50%)
Modeling Hemophilia
Time (s)
50 100 150 200 250 300
Thrombin (M)
0
1e-8
2e-8
Hemophilia A (1%)
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Thrombin (M)
8.0e-8
1.0e-7
1.2e-7
1.4e-7
Factor V Leiden(APC Resistance)
Modeling Hypercoagulable States
Time (s)
50 100 150 200 250 300
Thrombin (M)
0.0
2.0e-8
4.0e-8
6.0e-8
8.0e-8
Normal
Protein C Deficiency
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Modeling Therapeutic Intervention: Warfarin Treatment
Thrombin (M)
3e-8
4e-8
No Warfarin
Early Warfarin Treatment
Time (s)
50 100 150 200 250 300
Thrombin (M)
0
1e-8
2e-8
Warfarin Steady-State
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Network Architecture Determines Drug of Choice
X11
X1
With Feedback
No Feedback
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Modeling Temporo-Spatial Cellular Processes
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Summary
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This session will introduce practicing pathologists, pathologists in training, and
laboratory professionals to the concepts of
• the basics of cutting-edge Omic technologies,
• the basics of genomics, transcriptomics, proteomics, and metabolomics,
• next generation DNA and transcriptome sequencing,
Our Goals for this Course
• next generation DNA and transcriptome sequencing,
• the significance of cancer genome alterations for personalized treatment
decision making,
• mass spectrometry as an up and coming exciting enabling technology to look at
proteomes of diseased tissues, and
• the pathologist's key role in optimal large-scale biospecimen banking for
molecular pathology and research.
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DNA
RNA
Transformative Pathology: Training Molecular Physicians of the Future
Data Source Technology Data Analysis
Data InterpretationRNA
Proteins
Metabolites
Data Interpretation
Medical Action
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Next Generation Sequencing
Example workflow for Illumina sequencing
Target selection:
Whole genome
Exome
RNA
Custom
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Medical Impact of Exome Sequencing – An Example
Let’s look at the Methods section – now it is much clearer!!!
shotgun library
in-solution exome capture
Tiacci et al. NEJM, 2011
next gen sequencing
yes
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RNA-Seq: Whole Transcriptome Shotgun Sequencing
Wang et al. Nat Rev Genetics, 2009
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Mass Spectrometry in Pathology
MALDI Imaging
(“Histology by MS”)
Schwamborn and Caprioli. Nat Rev Cancer, 2010
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IEF & SDS-PAGE
:
Proteomic Analysis of Surgical Tissue
Tandem-MS/MS
Roehrl et al.
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Metabolomics in Pathology
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Pathology Takes
Center Stage
Transformative Pathology and Biospecimen Science
Diagnostics
Biospecimens
Center Stage
Pathology meets with the patient and
owns the informed consent process (>95%
consent rate)
Basic Biomedical Research
BankingBioinformatics and
Database Structures
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Outlook
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Integrating Personalized Cancer Genomes
Exome sequence (>30× coverage)
Personalized database representing all
patient-specific aberrations
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Integrating Personalized Cancer Genomes
Exome sequence (>30× coverage)
Personalized database representing all
patient-specific aberrations
Personalized functional characterization
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Morphologic snapshot(LM, EM, IHC, MP)
Omic snapshot
Genome sequencing
Transcriptome
Proteome
Metabolome
Transformative Pathology
• Dynamics
• Tumor heterogeneity
• Treatment response monitoring
• Differential treatment sensitivity
Ex vivo bioreactor
Stem cell isolation
Systems perturbation
(small molecules, siRNA)
Quantitative model building and data integration
Systems Pathology
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Acknowledgements
Julia Y. Wang
Dan Remick
Jung-hyun Rho
Sidney Wang
BMC Pathology and Laboratory Medicine
Channing Laboratory, Brigham and Women’s
Hospital
MIT, Francis Bitter Magnet LabSidney Wang
Robert Pistey
Brian Japp
Cheryl Spencer
Kathy Tilton
MIT, Francis Bitter Magnet Lab
National Institutes of Health
American Cancer Society
Karin Grunebaum Cancer Research Foundation
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Thank you for attending this brand new course!
I am looking forward to your thoughts, comments,
and suggestions!
Michael H. A. Roehrl, M.D., Ph.D.
Curious for more? NEW Systems Pathology Short Course:
USCAP Meeting, Vancouver, March 2012