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- 1. Expert center as a private public partnership ‐The complexity of The complexity of technologies in an SME structure for expert centers ‐ Th E The Europroteome experience‐ The Europroteome experience‐ t i Dr. Paul von Hoegen Dr Paul von Hoegen Managing Director Euraccine Consulting Group Brussels, Belgium Euraccine_be@yahoo.com +32 475 913572
- 2. Experience as CSO Europroteome Experienceas CSO Europroteome Colon Cancer Biobank for marker/target discovery with patient history and outcome p prediction • Academic network: High fluctuation – constant training • Needed samples rare – create meaningful patient groups • Technologies – constant development and changes from providers: Need to generate internal standards •Drug targets, biomarker, diagnostics, individualized therapy • Complexity: Multiple technologies and Integration of d f Bioinformatics (PhaseIt) • Investors and Industry clients: Wanted to see ready to go Biobank; No patients to build Biobank • Improve management of expectations Euraccine Consulting Group (Brussels) ‐ Paul von Hoegen 2
- 3. Pharma’s Needs 2003+ Needs • Anything that reduces development risk, time & costs: FAIL EARLY – FAIL CHEAP • Priorisation of (genomically derived) targets (500 – 5,000) to deal with the VALIDATION BOTTLENECK • COMPOUNDS • VALIDATED cancer targets (in vitro and in vivo) with link to a PATHWAY • Diagnostic bio-markers related to clinical OUTCOME • Identification of risk groups with ADVERSE EVENTS Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 4. Patient Centered Solutions Patient Centered Solutions DIAGNOSTICS THERAPY FOLLOW UP DEVELOPMENT Disease Marker Responder Profiling OncoAssist Biomarker Screening Assays Follow Up Therapy Control Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 5. CCN: Large Scientific Network g • Outstanding scientific and Outstanding scientific and medical expertise as sounding board for research Berlin (Hennigsdorf) (Hennigsdorf) results Hamburg Kiel Magdeburg Dortmund Stettin • „Breeding & sourcing Berlin (Charité) (Charité) ground for high‐calibre ground“ for high calibre Stuttgart Rennes Magdeburg product approaches Lausanne Cottbus Geneva Leipzig • Access to human tissue Access to human tissue Halle samples, pathology and Erlangen Lyon related patient data Grenoble Zurich CCN Bologna Chile THE CLINICAL CANCER NETWORK Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 6. Sampling Prior to surgery • Patients consent • Blood sampling; Stool sampling Surgery g y Pathology gy Histology * Pathological findings • Grading • pTNM (UICC) • etc. Cell sampling* Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) * Photos of kidney tissue/cells by Prof. F. Dombrowski, Pathology, Magdeburg
- 7. Human Tissue Sample Bank p 6.000 5.000 N umber of Samples s 4.000 3.000 3 000 f 2.000 1.000 0 Time Jan 01 Jan 02 Jan 03 Status as of March 10, 2003 Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 8. ONCOTRACK CLINICAL CANCER RECORDS & Features OUTCOMES DATABASE Colon, Stomach & Pancreas Cancer (number of variables) • Anamnesis and Diagnostics (48) • Surgery & Therapy (50) • Pathology (103) • Follow Up (21) • Local Recurrence (10) Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) • Distant Metastasis (6)
- 9. Cell Samples/Organ p / g Number of Patients: Number of Patients: Colon Rectum Stomach Liver Lung Pancreas Small Bowel Oesphagus Kidney plus ovar, bone, gallbladder Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) Status as of March 10, 2003
- 10. Research Matrix: Technologies g CHARAC- IDENTIFICATION VALIDATION TERIZATION B I O I N F O R M A T I C S 2D-PAGE MASS SPEC MASS SPEC CIPHERGEN SELDI DNA MICRO ARRAY & ROSETTA RESOLVER PROTEIN CHEMISTRY RT-PCR CELL CULTURE YEAST-2-HYBRID BIACORE Si RNA R E S O U R C E M A N A G E M E N T Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 11. Technologies for Cancer Target Identification via 2D‐PAGE & MS IEF SDS‐PAGE Staining Scanning Image Analysis Image Analysis Spot Picking MS Analysis Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 12. Colon Cancer Gene Expression Analyses: Proof of Concept MD134 MD149 MD150 MD135 MD133 MD121 20 CRC Patients MD82 C109 C141 C174 C139 C171 C118 106 113 112 C87 97 95 C86 C9 C9 E1 E1 E1 M M M M M M M EP-03-01 (DD Mode) MYC TIMP1 GAPDH CA1 FABP1 KRT19 KRT20 MUC2 CEACAM1 Color Range Scale EP-03-01: Induced transmembrane protein MYC: myc oncogene TIMP1: Tissue inhibitor of metalloproteinases 1 GAPDH: Glycerolaldehyde-3-phosphate dehydrogenase Up-regulated U l t d CA1: Carbonic anhydrase Down-regulated FABP1: Liver fatty acid binding protein KRT19: Cytokeratin 19 No gene regulation KRT20: Cytokeratin 20 MUC2: Mucin 2 CEACAM1: CEA related adhesion molecule 1 *Literature data are from human colon cancer tissue DNA microarray, SAGE and Northern blot experiments Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 13. … Combining Proteomics & Transcriptomics • Gene Profiling Data • 2D PAGE Data MD134 MD149 MD150 MD135 MD133 MD121 MD82 C109 C141 C174 C139 C171 C118 E106 E113 E112 C87 C97 C95 C86 C C C C C C C C C C KRT20 CA1 CA1 KRT20 FABP1 KRT20 Color Range Scale Up-regulated Down-regulated FABP1 No gene regulation pH 5-8; patient tumor sample SwissProt # Protein name Literature* reported data EP data 2D PAGE data DNA array/SAGE data 2D PAGE DNA array P00915 Carbonic anhydrase I (CA1) down down up/down up/down P07148 Liver fatty acid binding protein (FABP1) down down down down P35900 Keratin cytoskeletal 20 ( y (KRT20)) down down up/down down * Literature data are from the experiments with human colon cancer tissue Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 14. Colon / Metastasis Screen Tissue Serum Colon Rectum Colon Rectum with metastasis 6 3 20 0 number of patients without metastasis 12 8 16 0 Colorectal cancer specimens Serum Transcriptomics Proteomics 289 differences d ff 223 differences 223 diff 37 differences (2 fold change; (2 fold change; p‐value < 0.01) 40% frequency) FPLC/HPLC Identification In silico validation In silico validation Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 15. Classification of regulated proteins (Who needs what?) (Wh d h t?) Cytokeratins Proteases 4% 5% Ribosomal Kinases 1% Other 1% Nucleic Acid 11% Structural/Cell Binding adhesion 2% 12% Immunoglobulines Transport/ (and related) Processing/ P i / 5% Chaperone Function 10% Enzymes 49% Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 16. Target Identification & Selection Target Identification & Selection Will vary for each application (client), combined with bioinformatics Extensive annotation and 3 project potential Complex annotation, 10 Target profile Target profile DNA Array, > 50 Bioinformatics > 350 2D, MS 2D MS # of Targets (example) Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 17. Research Matrix: Technologies g CHARAC- IDENTIFICATION VALIDATION TERIZATION B I O I N F O R M A T I C S 2D-PAGE MASS SPEC MASS SPEC CIPHERGEN SELDI DNA MICRO ARRAY & ROSETTA RESOLVER PROTEIN CHEMISTRY RT-PCR CELL CULTURE YEAST-2-HYBRID BIACORE Si RNA R E S O U R C E M A N A G E M E N T Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 18. Cancer Target Validation Cancer Target Validation Binding Partners (BiaCore) Yeast Culture (Y‐2‐H) Cell Culture (siRNA, anti sense) Cell Culture (siRNA, anti sense) Data Integration Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 19. Validation: The Technology Wheel Validation: The Technology Wheel Antibodies 2D gels 2D gels Yeast 2 Hybrid Mass Spectrometry 3 12 RNAi DNA Arrays 48 RT PCR >350 Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) Cyphergen
- 20. Cancer Target Discovery Status Cancer Target Discovery Status Seldi Markers Membrane Targets Stomach/Colon 3 Colon Metastasis 12 48 > 350 Stomach Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 21. Colorectal Cancer: Gene Expression Breakdown by UICC Stage* • Pre‐UICC Stage III – 112 preferred marker genes expressed preferred marker genes expressed • UICC Stage III – 319 preferred marker genes expressed f d k d • UICC Stage IV – 907 preferred marker genes expressed Up/Down ratio: Clearly negative *preliminary data based on a limited no. of analysed samples Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 22. … as Tool for Functional Target Validation 100 UICC stage I UICC stage I Risk 0 90 Risk 1 UICC I 80 70 • Decision system based on artificial intelligence Percent Survival 60 50 40 • Classification of high‐risk patients 30 for distant metastasis possible 20 10 • Based on only 6 clinical 0 parameters 0 12 24 36 48 60 72 84 96 108 120 132 144 156 168 180 192 204 100 Survival (months) Risk Ri k 0 90 UICC stage II Risk 1 UICC II 80 • Tool to be positioned to identify 70 high‐risk patients in Stage I & II vival 60 Percent Surv 50 • Discussions with pharma 40 companies for application 30 20 10 0 0 12 24 36 48 60 72 84 96 108 120 132 144 156 168 180 192 204 Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) Survival (months)
- 23. From Disease Centered Biobank Research .. CytosolicProteins Seldi Proteins Histopathology Membrane Proteins tumor cell HLA- assoc. Peptides cDNA Microarray Clinical Data Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 24. ...To Patient Centered Solutions To Patient Centered Solutions DIAGNOSTICS THERAPY FOLLOW UP PROGNOSTICS DEVELOPMENT Disease Marker Responder Profiling OncoAssist ONCOTRACK ONCOASSIST CLINICAL CANCER RECORDS & OUTCOMES DATABASE CANCER OUTCOME PREDICTION & STRATIFICATION Screening Assays Follow Up ONCOPREP CCN CANCER CELL PURIFICATION THE CLINICAL CANCER NETWORK Therapy Control Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 25. Life event history calendar for collecting detailed patient information d il d i i f i Standardized set of cues offer conceptual Standardized set of cues offer conceptual anchors (such as important life themes or domains, e.g., life relationships, jobs, residences, etc.) and encourage top‐down , ) g p processing. Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 26. LEHC: Parallel Processing of patient information: Complete history of lifestyle and disease possible Complete history oflifestyle and disease possible Parallel processing : balanced visual organization allows the individual to look at the display, use cues from their own life, and remember events base on their interrelationships between domains. Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 27. Expectations / Ideas / Challenges p / / g •Integrate all players (patients, ethics academic, agencies, service g p y (p , , g , provider and end-user) •Assure long time engagement under constant conditions •Manage change and integration of new technologies Manage •Multiple platforms for identification and validation •Individual marker versus patterns – making the choice •Standards and reference samples for ring validations •Priorities for sample distributions? How to conserve the material best for the future? •Longitudinal follow up of disease markers (same patient) •Links to clinical trials and treatment outcome •Foresee the needs of the future (of the partners) Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 28. Biotech, Start ups Biotech example Technology Academic providers Research Dr. Paul von Hoegen Euraccine Consulting Group (Brussels)
- 29. Need of strong Core Assets Need of strongCore Assets BBMRI Confid C Dr. Paul von Hoegen Euraccine Consulting Group (Brussels) ality dentia