PROTÉOMIQUE. Application de la protéomique à la cartographie de l interactome et la découverte de biomarqueurs. BENOIT COULOMBE, PhD

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1 PROTÉOMIQUE Application de la protéomique à la cartographie de l interactome et la découverte de biomarqueurs BENOIT COULOMBE, PhD Laboratoire de protéomique & transcription génique BCM2003, mars 2012

2 Biomarkers and personalized medicine Early diagnosis and prognosis of disease Monitoring the response of patients to treatment - Known therapies - Development of new drugs Stratification of patient cohorts in order to provide personalized treatments for specific disease phenotypes (ex: IRESSA and lung cancer) Process of biomarker discovery can also identify new targets for drug discovery, and develop new knowledge on mechanisms of disease

3 The sequencing of the human genome has provided the list and linear sequence of all (most) human proteins Genome Proteins

4 Proteins rarely work alone, but rather assemble into protein complexes that integrate the function of multiple gene products Genome Proteins Complexes Machineries Function

5 Large-scale genomic studies identify an increasing number of genes associated with disease phenotypes Genome

6 Large-scale genomic studies identify an increasing number of genes associated with disease phenotypes Genome How the products of these genes participate in the establishment and the progression of disease is often unknown!

7 The interaction partners of disease-associated proteins can reveal their role in disease (guilt by association) Genome Proteins Complexes Machineries Role in disease

8 The interaction partners of disease-associated proteins are likely to act as modulators of the disease phenotype Genome Proteins Complexes Modulators Machineries Role in disease

9 The disease-associated proteins and their interactors are putative biomarkers and drug targets Genome Proteins Complexes Biomarkers Drug targets Machineries Role in disease

10 1. Laboratory Pipelines The P3MD platform Infrastructure, expertise, and data A. INTERACTOME B. BIOMARKERS Selection of Disease-Associated Proteins (Baits) AP-MS Selection of Peptides (transitions) SRM Cell Lines Candidate Biomarkers Patient Samples 2. Software Applications PROTEUS Candidate Biomarker Selection Engine P3MD Computational tools Computational classifier 3. Data List of Interactions (Network Maps) List of Validated Biomarkers

11 The human proteome

12 Identification of an association between a protein and a disease The case of hypothetical protein D D

13 The protein D interactome D

14 High-quality generic map of the protein D interactome Affinity purification coupled with MS D

15 Components of the protein D interactome are candidate drug targets and biomarkers D

16 Identification of interactors using LC-MS/MS + Determination of a probability (False Discovery Rate or FDR) for each interaction to be valid using computational algorithm trained using machine learning to differentiate valid vs. invalid interactions

17 Components of the protein D interactome are candidate drug targets and biomarkers D

18 Components of the protein D interactome are candidate drug targets and biomarkers D I

19 Components of the protein D interactome are candidate drug targets and biomarkers D I I

20 Preliminary validation of candidate biomarkers Modulations of components of protein D interactome in disease cells (SRM) D Upregulated Isoform Downregulated

21 Selected Reaction Monitoring (SRM, also termed MRM) Protein quantification is possible by spiking known amounts of chemically synthesized heavy-labelled peptides in the samples (standard)

22 Proof of concept

23 Cellular machineries involved in mrna synthesis GENERAL TRANSCRIPTION MACHINERY - RNA polymerase II (RNAP II) - General transcription factors - Elongation factors TFIID Mediator TFIIF RNAP II P-TEFb TFIIF RNAP II TFIIS 5 TATAAA +1 3 TFIIB TFIIE TFIIH Cleavage/polyA factors CHROMATIN-REMODELING MACHINERY - ATP dependent remodeling - Histone-modifying enzymes PRE-mRNA snrnps U1-U6 hnrnps PRE-mRNA PROCESSING MACHINERY Capping enzymes

24 Cellular machineries involved in mrna synthesis GENERAL TRANSCRIPTION MACHINERY - RNA polymerase II (RNAP II) - General transcription factors - Elongation factors TFIID Mediator TFIIF RNAP II P-TEFb TFIIF RNAP II TFIIS 5 TATAAA +1 3 TFIIB TFIIE TFIIH Cleavage/polyA factors CHROMATIN-REMODELING MACHINERY - ATP dependent remodeling - Histone-modifying enzymes PRE-mRNA snrnps U1-U6 hnrnps PRE-mRNA PROCESSING MACHINERY Capping enzymes

25 A platform for the systematic characterization of protein interaction networks in human cells Collection of 293 cell lines engineered to express physiological levels of affinity tagged polypeptides upon induction Soluble fraction (supernatant) Cell Lysis in Mild Conditions Insoluble fraction (pellet) Main Features of the Procedure: 1) Expression at physiological level 2) Cell lysis in mild conditions (soluble) 3) Purification in native conditions 4) Protein identification by sensitive MS 5) Efficient data analysis and validation Protein Identification Computational Analysis (Reliability, Connectivity)

26 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision)

27 The ecdysone-inducible mammalian expression system pvgecr pind Modified from Vickers and Sharrocks, 2002 Advantages: very low basal expression ecdysone analogs are inert in mammalian cells high control on expression levels (physiological) Western blot

28 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision)

29 Tandem affinity purification in native conditions Double-affinity tagged protein extract Protein of interest Calmodulin binding peptide (CBP) TEV protease cleavage site Protein A IgG-binding sites IgG sepharose Double-affinity Tag Unbound Bound TEV protease IgG Sepharose Beads Eluate Unbound Calmodulin Beads Bound TEV Beads EGTA Eluate Calmodulin Beads Purified Protein Complexes EGTA

30 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision)

31 Identification of proteins by mass spectrometry SDS- PAGE Excised proteins Trypsin digestion Peptides mixture In-gel digestion N-I I Yarmush and Jayaraman, 2002

32 Mass spectrometry Peptide Sequence LC-MS/MS Computer Cluster

33 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision)

34 Affinity purification of protein complexes

35 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification Reciprocal tagging SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision)

36 Reciprocal tagging allows to validate some interactions and to enrich the data set

37 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification Reciprocal tagging SDS gel analysis (high resolution) Protein identification (Orbitrap MS: high sensitivity & mass precision) Computational analysis (reliability & connectivity)

38 A platform for the systematic characterization of protein interaction networks in human cells Human cdna cloned into an ecdysone-inducible expression vector encoding the TAP tag Transfection in EcR-293 cells and selection of expressing clones Induction with ponasterone A to obtain near physiological expression levels Cell lysis in mild conditions Centrifugation Soluble fraction (WCE) Insoluble fraction (pellet) Tandem Affinity Purification Reciprocal tagging SDS gel analysis (high resolution) Comprehensive Maps of Human Protein Interaction Networks Protein identification (Orbitrap MS: high sensitivity & mass precision) Computational analysis (reliability & connectivity)

39 The protein interaction database Proteus C. Poitras & D. Bergeron

40 Computational data analysis and validation A B C

41 Computational data analysis and validation keeping 83% of the interactions supported by the literature excluding 83% of the interactions judged likely false-positives

42 Summary of our survey of protein complexes (2007) 805 distinct interactions were selected as high-confidence protein interactions Jeronimo et al (2007) Mol Cell 27, 262

43 High-quality protein interaction network for the RNA polymerase II transcription machinery

44 Proof of concept

45 Myopathies The myopathies are a heterogeneous group of diseases of skeletal muscle They include: Sporadic Inclusion-Body Myositis (sibm) Dermatomyositis Polymyositis Myofibrillar myopathies Neurogenic muscular athrophy IBMPFD And many others

46 The RNA Polymerase II-Associated Proteins (RPAPs) are previously uncharacterized proteins

47 Expression of components of the RNAPII network is specifically modulated in tissues of patients suffering from various muscular diseases Muscle disease N biopsies RPAPx RPAPy RPAPz Normal controls 15 Normal Normal Normal Disease Phenotype A 12 Increased * Normal Normal Disease Phenotype B 8 Increased Increased * Increased Disease Phenotype C 10 Increased Normal Increased Increased expression of RPAPs is the only marker today that permits to discriminate between two specific muscular disorders

48 The RPAPs are dysregulated in muscular diseases

49 Diseases under study Myopathies Leucodystrophies Type 2 diabetes and insulin resistance Hypercholesterolemia Cancer

50 Thank you!