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

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May 25, 2023 175 likes •529 views

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

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Molecular profiling of RCC: Timeless lessons

Gennady Bratslavsky, M.D.

Professor and Chairman

Department of Urology Upstate Medical University Syracuse, NY

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DISCLOSURES: NONE

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The Urologic Oncology Branch at the National Cancer Institute

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SUNY Upstate Medical University Department of Urology

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Human Renal Epithelial Neoplasms

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

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M E T

PI3K FLCN

FNIP1 FNIP2

PTEN TFE3 TSC2 TSC1 Rheb LKB1 AMPK

mTORC2

Akt

mTORC1 HIFα

VHL PHD FH SDH

Hsp90 Hsp90 Hsp90 Hsp90 Hsp90 Hsp90 Hsp90 Hsp90

Clear cell Papillary Type 1 Papillary Type 2 TFE3 Onco- cytoma Hybrid Chromo- phobe Oncocytic Angiomyolipoma Clear/Chromophobe

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Molecular Profiles

Transcription

DNA

Translation

RNA

PTM

Protein

Transcriptome Proteome Genome

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Interrogation of DNA (Genome)

 Sequencing, mutational analysis, gene

losses/gains

 DNA methylation /gene silencing  Cell Free DNA

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Nature, 2013

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Chromosomal analysis and gene methylation in RCC

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Interrogation of RNA (transcriptome)

31,910 Publications on Gene Signatures!

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Interrogating MicroRNA (miRNA)

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 Tens of thousands articles evaluating protein

levels, levels of expression, immunohistochemistry, interactions, post- translational modifications, pathways, etc

Interrogating proteome

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Nogueira M et al. Urologic Oncology

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Interrogating metabolome

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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?

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My own journey with BIG DATA

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Sanford-Bratslavsky. Plos One

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Biobanking quality matters

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

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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

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One More Variable

LAPAROSCOPY/ROBOTICS

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Laparoscopic/Robotic Surgery

 Tissue procured from laparoscopic/robotic

procedures is subjected to ischemia time at body temperature

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Methods – Tissue Procurement

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Snap frozen a piece (time = zero) 4ºC - Ice 22ºC - Room 37ºC – Laparoscopy 5 30 60 120 240 5 30 60 120 240 5 30 60 120 240 Snap frozen at these time points (mins)

16 samples per tumor

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0 5 30 60 120 240 5 30 60 120 240 5 30 60 120 240

Time (mins) 4ºC 22ºC 37ºC Temperature (ºC)

Gel Electropheresis of Tumor RNA

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Time point = 0 mins t = 5 mins t = 30 mins t = 60 mins t = 120 mins t = 240 mins 4ºC 22ºC 37ºC

18S 28S

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Differentially Expressed Genes

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Concept of branched evolution and heterogeneity

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Bratslavsky et al, J Cancer, 2011

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Please separate tumor heterogeneity from heterogeneity of quality

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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

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