1. Tissue Microarrays In Biomarker Discovery and Development Stephen M. Hewitt, MD, PhD Tissue Array Research Program National Cancer Institute, NIH, USA Annual Meeting 2005

2. Integrated “-omic” Analysis

3. Translational Medicine Basic Science Translational Medicine Clinical Medicine Adapted from D.L. Farkas Nat. Biotechnol.21, 1269

4. Biomarker Development • Discovery • Small Sample Numbers • Complex Assays • Development Of Assays • Validation • Large Cohorts • Multiple Cohorts • Hardened Assays • Extending The Initial Question • Introduction To Clinical Use

5. Biomarkers: Better, Faster, Cheaper • Must Add Utility • Be Applicable To Current Care Environment • Tissue Based Biomarker Assays • Transcriptomics • Proteomics • Immunohistochemistry

6. Formalin Fixed, Paraffin Embedded Tissue • Common Platform For Histo-morphology • Based On Over 100 Year Fund Of Knowledge • Reproducible Artifact • RNA, DNA & Protein Can Be Extracted • Expression Arrays, RT-PCR • SNP Analysis, PCR • Peptide Arrays, Mass Spec

7. The Future Of FFPE Tissue • Standardize The Process • Tissue Handling • Tissue Fixation • Tissue Processing • Optimize The Assays • Immunohistochemistry • Nucleic Acid Extraction Methods

8. What Is A Tissue Array? NCI TARP LAB TARP2 C-052 • A Block Of Samples From Hundreds Of Blocks • Multiple Samples • Paraffin Embedded Or Frozen Tissue • Arranged In An Organized Fashion • Platform For High- Throughput Pathology

9. From Tissue To Arrays • Develop Hypothesis • Identify Tissue • Prepare Tissue • Array Tissue • Section Arrays • Perform Experiment • Analyze Data • Publish • Repeat

10. Instrumentation Continues To Evolve Labor Intensive Histotechnologist Best Implemented In A Core Facility MTA-1 Tissue Arrayers

11. Removing The Blank Core From The Recipient Block Arraying

12. Mapping Donor Block Arraying

13. Removing The Core Of Donor Tissue Arraying

14. Placing The Donor Core In The Recipient Block Arraying

15. Donor Block After Arraying Arraying

16. Recipient Block After Arraying Arraying

17. Arraying The Correct Tissue • A Fresh Section Is Cut And H&E Made • The Section Is Reviewed, And The Target Tissue Is Outlined • Smallest Reasonable Target ~ 1.5 mm • When Arraying, The Slide Is Overlaid With The Block

18. Quality Is Everything • Donor Tissue Quality • Histology • Proteins • Nucleic Acids • Array Quality • Clinical Data • Complete • Detailed

19. Uses Of Tissue Microarrays • Immunohistochemistry 95% • In Situ Hybridization 4% • Other 1%

20. Challenges In The Process Of Building A TMA • Identifying Adequate/Appropriate Material • Negotiating MTA/IRB Approval • Specimens Present Special Challenges • Biopsy & Small Specimens Are Hard To Array • Prior Use Of Material For Research • Diversity Of Specimen Sources • Regional Differences In Diagnosis & Treatment • Differences In Specimen Handling • Informatics • Managing Expectations • Pathologist Vs Scientist

21. Multifaceted Role Of TMAs In Translational Research CMAs XMAs TMAs

22. CMAs Cell Line Microarrays • Western On A Chip Approach • Rapid Screening Of Protein Expression • Validated Antibody • Pathway Toward Screening In Tissue

23. XMAs Xenograft Microarrays • Similar Uses As CMAs • Provides Context Of Tissue • Primary Use: • Pathway Analysis • Drug Development • Model Systems Of Rare Tumors

24. TMAs - Tissue Microarrays • Wide Utility • Validation Of Results From Other Platforms • Pathway Analysis • Drug Development • Biomarker Development • Model Systems – Other Animals • Complexity Of Tissue • Heterogeneity • Descriptive Analysis

25. TMAs & Translation Research • High-Throughput Pathology Is Essential • Automation Of Data Collection & Analysis Are Currently The Limiting Factors • Reduction To Utility Continues To Require Manual Interpretation • Correlation With Outcome Essential • Requires Follow-Up • Greater Attention To Collection Of Tissue

26. In Vitro Screening Methods Clinical Trials Epidemiology Based Studies Multi-tumor Systems Other Methods Micro-Arrays Tissue Microarrays Validation In Real Patient Samples Pathways To TMAs In Biomarker Development

27. Acknowledgements • Kimberly Tuttle • Mikiko Takikita • Joon Yong Chung • Till Braunschweig • Yvonne Gathright • Marsha Reichman • Mark Sherman • Phil Taylor • Phil Dennis • Chand Khanna • Javed Khan • Robert Star • Developmental Therapeutics Program

28. Tissue Array Research Program http://cancer.gov/tarp/ genejock@helix.nih.gov TARP Lab Advanced Technology Center MSC 4605 Bethesda, MD 20892-4605