Timeless lessons Gennady Bratslavsky, M.D. Professor and Chairman - PowerPoint PPT Presentation

Molecular profiling of RCC: Timeless lessons Gennady Bratslavsky, M.D. Professor and Chairman Department of Urology Upstate Medical University Syracuse, NY

DISCLOSURES: NONE

The Urologic Oncology Branch at the National Cancer Institute

SUNY Upstate Medical University Department of Urology

Human Renal Epithelial Neoplasms Papillary Chromophobe Oncocytoma Type: Clear Cell Papillary Hybrid Type 2 Type 1 Gene: VHL BHD MET FH Type: Clear/Chromophobe Angiomyolipoma Oncocytic TFE3 SDHB, SDHC, Gene: TFE2,TFEB PTEN TSC1,TSC2 SDHD

Papillary Type 1 M Clear/Chromophobe E T Hsp90 PTEN TFE3 PI3K LKB1 Hybrid AMPK Akt TFE3 Hsp90 Chromo- Onco- mTORC2 phobe cytoma Angiomyolipoma FNIP1 FNIP2 Hsp90 TSC2 FLCN Hsp90 TSC1 Hsp90 Papillary Type 2 Oncocytic FH Hsp90 Rheb Hsp90 SDH Clear cell mTORC1 PHD HIF α VHL Hsp90

Molecular Profiles DNA RNA Protein Transcription Translation PTM Genome Transcriptome Proteome

Interrogation of DNA (Genome)  Sequencing, mutational analysis, gene losses/gains  DNA methylation /gene silencing  Cell Free DNA

Nature, 2013

Chromosomal analysis and gene methylation in RCC

Interrogation of RNA (transcriptome) 31,910 Publications on Gene Signatures!

Interrogating MicroRNA (miRNA)

Interrogating proteome  Tens of thousands articles evaluating protein levels, levels of expression, immunohistochemistry, interactions, post- translational modifications, pathways, etc

Nogueira M et al. Urologic Oncology

Interrogating metabolome

Important concepts  Molecular profiling: the concept from BIG data (sequencing, arrays, large screens)  How good is the data?  How reproducible is it?  What drive these data?

My own journey with BIG DATA

Sanford-Bratslavsky. Plos One

Biobanking quality matters HUNDREDS / THOUSANDS OF GENES ARE AFFECTED BY PROCUREMENT CONDITIONS AND STORAGE

Tissue Procurement Conditions  Personalized/Precsision Medicine depends on accurate expression profiling of surgical specimens  Standardized guidelines on tissue processing after surgical extirpation are lacking  Methods of tissue acquisition alone could significantly impact tumor profile

One More Variable LAPAROSCOPY/ROBOTICS

Laparoscopic/Robotic Surgery  Tissue procured from laparoscopic/robotic procedures is subjected to ischemia time at body temperature

Methods – Tissue Procurement

16 samples per tumor Snap frozen a piece (time = zero) 4 º C - Ice 37 º C – Laparoscopy 22 º C - Room 5 30 60 120 240 5 30 60 120 240 5 30 60 120 240 Snap frozen at these time points (mins)

Gel Electropheresis of Tumor RNA Time (mins) 0 5 30 60 120 240 5 30 60 120 240 5 30 60 120 240 4 º C 22 º C 37 º C Temperature ( º C)

28S 18S Time point = 0 mins 4 º C 22 º C 37 º C t = 5 mins t = 30 mins t = 60 mins t = 120 mins t = 240 mins

Differentially Expressed Genes

Concept of branched evolution and heterogeneity

Bratslavsky et al, J Cancer, 2011

Please separate tumor heterogeneity from heterogeneity of quality

Conclusions  Molecular profiles are the ultimate path for risk stratification, prognostication, and therapy selection  Molecular profiles are highly dependent on high quality tissue preservation  With existing heterogeneity of RCC genetics high quality biobanking will allow for future progress