Literature DB >> 32220885

Comprehensive Genomic Analysis of Translocation Renal Cell Carcinoma Reveals Copy-Number Variations as Drivers of Disease Progression.

Renzo G DiNatale1, Alejandro Sanchez1, A Ari Hakimi2, Ed Reznik3,4, Julian Marcon1, Ritesh R Kotecha5, Sounak Gupta6, Fengshen Kuo7, Vladimir Makarov7, Amar Sandhu8, Roy Mano1, Andrew W Silagy1, Kyle A Blum1, Daniel E Nassau1, Nicole E Benfante1, Michael V Ortiz9, Maria I Carlo5, Timothy A Chan7,10, Robert J Motzer5, Martin H Voss5, Jonathan Coleman1, Paul Russo1, Victor Reuter6.   

Abstract

PURPOSE: Translocation renal cell carcinoma (tRCC) is a rare, aggressive renal cell carcinoma (RCC) subtype. There is currently limited understanding on the role of molecular alterations in the pathogenesis and progression of these tumors. We investigated the association between somatic alterations and clinical outcomes in two independent cohorts profiled using DNA sequencing. EXPERIMENTAL
DESIGN: Twenty-two tRCCs underwent targeted sequencing [Memorial Sloan Kettering Cancer Center (MSK)-IMPACT]; a subset was profiled using exome-sequencing and combined with exome data from The Cancer Genome Atlas (TCGA) for analysis. The prognostic value of specific somatic aberrations, tumor mutation burden (TMB), and fraction of copy-number-altered genome (FCNAg) was explored. In TCGA cases, neoantigen prediction and immune cell deconvolution were performed using RNA-sequencing and exome data. Overall survival estimates were computed using the Kaplan-Meier method; time-on-treatment was calculated for 14 MSK-IMPACT patients who underwent systemic therapy. Associations between molecular features and outcomes were evaluated using nonparametric testing.
RESULTS: Copy-number aberrant tRCCs were associated with poor overall survival (P = 0.03). Pediatric patients had tumors with lower FCNAg (P = 0.01). In one adult case with two chronologically distinct tumor samples sequenced, we confirmed that copy-number events occurred early during evolution. TERT promoter mutations were found exclusively in high-stage tumors. We found that tRCCs displayed distinct angiogenesis and PD-L1 gene expression profiles compared with other RCC subtypes.
CONCLUSIONS: Tumors molecularly defined by increased copy-number variations were associated with aggressive disease in tRCC. A higher burden of genomic events in adults compared with pediatric cases likely reflects a more aggressive clinical course. The unique immunophenotypic characteristics of tRCC merit further exploration. ©2020 American Association for Cancer Research.

Entities:  

Year:  2020        PMID： 32220885      PMCID： PMC7367714          DOI： 10.1158/1078-0432.CCR-19-3283

Source DB:  PubMed          Journal:  Clin Cancer Res        ISSN： 1078-0432            Impact factor:   12.531


  49 in total

1.  dbSNP: the NCBI database of genetic variation.

Authors:  S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  Translocation carcinomas of the kidney after chemotherapy in childhood.

Authors:  Pedram Argani; Marick Laé; Edgar T Ballard; Mahul Amin; Carlos Manivel; Brian Hutchinson; Victor E Reuter; Marc Ladanyi
Journal:  J Clin Oncol       Date:  2006-04-01       Impact factor: 44.544

3.  Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.

Authors:  Diana Miao; Claire A Margolis; Wenhua Gao; Martin H Voss; Wei Li; Dylan J Martini; Craig Norton; Dominick Bossé; Stephanie M Wankowicz; Dana Cullen; Christine Horak; Megan Wind-Rotolo; Adam Tracy; Marios Giannakis; Frank Stephen Hodi; Charles G Drake; Mark W Ball; Mohamad E Allaf; Alexandra Snyder; Matthew D Hellmann; Thai Ho; Robert J Motzer; Sabina Signoretti; William G Kaelin; Toni K Choueiri; Eliezer M Van Allen
Journal:  Science       Date:  2018-01-04       Impact factor: 47.728

4.  FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.

Authors:  Ronglai Shen; Venkatraman E Seshan
Journal:  Nucleic Acids Res       Date:  2016-06-07       Impact factor: 16.971

5.  Characterization and Impact of TERT Promoter Region Mutations on Clinical Outcome in Renal Cell Carcinoma.

Authors:  Jozefina Casuscelli; Maria F Becerra; Brandon J Manley; Emily C Zabor; Ed Reznik; Almedina Redzematovic; Maria E Arcila; Daniel M Tennenbaum; Mazyar Ghanaat; Mahyar Kashan; Christian G Stief; Maria Carlo; Martin H Voss; Darren R Feldman; Robert J Motzer; Yingbei Chen; Victor E Reuter; Jonathan A Coleman; Paul Russo; James J Hsieh; Abraham Ari Hakimi
Journal:  Eur Urol Focus       Date:  2017-09-24

Review 6.  Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different.

Authors:  Chung-Han Lee; Roman Yelensky; Karin Jooss; Timothy A Chan
Journal:  Trends Immunol       Date:  2018-05-08       Impact factor: 16.687

7.  OncoKB: A Precision Oncology Knowledge Base.

Authors:  Debyani Chakravarty; Jianjiong Gao; Sarah M Phillips; Ritika Kundra; Hongxin Zhang; Jiaojiao Wang; Julia E Rudolph; Rona Yaeger; Tara Soumerai; Moriah H Nissan; Matthew T Chang; Sarat Chandarlapaty; Tiffany A Traina; Paul K Paik; Alan L Ho; Feras M Hantash; Andrew Grupe; Shrujal S Baxi; Margaret K Callahan; Alexandra Snyder; Ping Chi; Daniel Danila; Mrinal Gounder; James J Harding; Matthew D Hellmann; Gopa Iyer; Yelena Janjigian; Thomas Kaley; Douglas A Levine; Maeve Lowery; Antonio Omuro; Michael A Postow; Dana Rathkopf; Alexander N Shoushtari; Neerav Shukla; Martin Voss; Ederlinda Paraiso; Ahmet Zehir; Michael F Berger; Barry S Taylor; Leonard B Saltz; Gregory J Riely; Marc Ladanyi; David M Hyman; José Baselga; Paul Sabbatini; David B Solit; Nikolaus Schultz
Journal:  JCO Precis Oncol       Date:  2017-05-16

8.  TumorFusions: an integrative resource for cancer-associated transcript fusions.

Authors:  Xin Hu; Qianghu Wang; Ming Tang; Floris Barthel; Samirkumar Amin; Kosuke Yoshihara; Frederick M Lang; Emmanuel Martinez-Ledesma; Soo Hyun Lee; Siyuan Zheng; Roel G W Verhaak
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

9.  Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

Authors:  Samra Turajlic; Hang Xu; Kevin Litchfield; Andrew Rowan; Stuart Horswell; Tim Chambers; Tim O'Brien; Jose I Lopez; Thomas B K Watkins; David Nicol; Mark Stares; Ben Challacombe; Steve Hazell; Ashish Chandra; Thomas J Mitchell; Lewis Au; Claudia Eichler-Jonsson; Faiz Jabbar; Aspasia Soultati; Simon Chowdhury; Sarah Rudman; Joanna Lynch; Archana Fernando; Gordon Stamp; Emma Nye; Aengus Stewart; Wei Xing; Jonathan C Smith; Mickael Escudero; Adam Huffman; Nik Matthews; Greg Elgar; Ben Phillimore; Marta Costa; Sharmin Begum; Sophia Ward; Max Salm; Stefan Boeing; Rosalie Fisher; Lavinia Spain; Carolina Navas; Eva Grönroos; Sebastijan Hobor; Sarkhara Sharma; Ismaeel Aurangzeb; Sharanpreet Lall; Alexander Polson; Mary Varia; Catherine Horsfield; Nicos Fotiadis; Lisa Pickering; Roland F Schwarz; Bruno Silva; Javier Herrero; Nick M Luscombe; Mariam Jamal-Hanjani; Rachel Rosenthal; Nicolai J Birkbak; Gareth A Wilson; Orsolya Pipek; Dezso Ribli; Marcin Krzystanek; Istvan Csabai; Zoltan Szallasi; Martin Gore; Nicholas McGranahan; Peter Van Loo; Peter Campbell; James Larkin; Charles Swanton
Journal:  Cell       Date:  2018-04-12       Impact factor: 41.582

10.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.

Authors:  Andy Rimmer; Hang Phan; Iain Mathieson; Zamin Iqbal; Stephen R F Twigg; Andrew O M Wilkie; Gil McVean; Gerton Lunter
Journal:  Nat Genet       Date:  2014-07-13       Impact factor: 38.330
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  7 in total

1.  Integrative clinical and molecular characterization of translocation renal cell carcinoma.

Authors:  Ziad Bakouny; Ananthan Sadagopan; Praful Ravi; Nebiyou Y Metaferia; Jiao Li; Shatha AbuHammad; Stephen Tang; Thomas Denize; Emma R Garner; Xin Gao; David A Braun; Laure Hirsch; John A Steinharter; Gabrielle Bouchard; Emily Walton; Destiny West; Chris Labaki; Shaan Dudani; Chun-Loo Gan; Vidyalakshmi Sethunath; Filipe L F Carvalho; Alma Imamovic; Cora Ricker; Natalie I Vokes; Jackson Nyman; Jacob E Berchuck; Jihye Park; Michelle S Hirsch; Rizwan Haq; Gwo-Shu Mary Lee; Bradley A McGregor; Steven L Chang; Adam S Feldman; Catherine J Wu; David F McDermott; Daniel Y C Heng; Sabina Signoretti; Eliezer M Van Allen; Toni K Choueiri; Srinivas R Viswanathan
Journal:  Cell Rep       Date:  2022-01-04       Impact factor: 9.995

2.  From Basic Science to Clinical Translation in Kidney Cancer: A Report from the Second Kidney Cancer Research Summit.

Authors:  Toni K Choueiri; Laurence Albiges; Michael B Atkins; Ziad Bakouny; Gennady Bratslavsky; David A Braun; Naomi B Haas; John B A G Haanen; A Ari Hakimi; Michael A S Jewett; Eric Jonasch; William G Kaelin; Payal Kapur; Chris Labaki; Bryan Lewis; David F McDermott; Sumanta K Pal; Kevin Pels; Susan Poteat; Thomas Powles; W Kimryn Rathmell; Brian I Rini; Sabina Signoretti; Nizar M Tannir; Robert G Uzzo; Hans J Hammers
Journal:  Clin Cancer Res       Date:  2022-03-01       Impact factor: 13.801

3.  Comprehensive data analysis of genomics, epigenomics, and transcriptomics to identify specific biomolecular markers for prostate adenocarcinoma.

Authors:  Chunwei Ye; Haifeng Wang; Zhipeng Li; Chengxing Xia; Shunhui Yuan; Ruping Yan; Xiaofang Yang; Tao Ma; Xingqiao Wen; Delin Yang
Journal:  Transl Androl Urol       Date:  2021-07

4.  New developments in existing WHO entities and evolving molecular concepts: The Genitourinary Pathology Society (GUPS) update on renal neoplasia.

Authors:  Kiril Trpkov; Ondrej Hes; Sean R Williamson; Anthony J Gill; Adebowale J Adeniran; Abbas Agaimy; Reza Alaghehbandan; Mahul B Amin; Pedram Argani; Ying-Bei Chen; Liang Cheng; Jonathan I Epstein; John C Cheville; Eva Comperat; Isabela Werneck da Cunha; Jennifer B Gordetsky; Sounak Gupta; Huiying He; Michelle S Hirsch; Peter A Humphrey; Payal Kapur; Fumiyoshi Kojima; Jose I Lopez; Fiona Maclean; Cristina Magi-Galluzzi; Jesse K McKenney; Rohit Mehra; Santosh Menon; George J Netto; Christopher G Przybycin; Priya Rao; Qiu Rao; Victor E Reuter; Rola M Saleeb; Rajal B Shah; Steven C Smith; Satish Tickoo; Maria S Tretiakova; Lawrence True; Virginie Verkarre; Sara E Wobker; Ming Zhou
Journal:  Mod Pathol       Date:  2021-03-04       Impact factor: 8.209

5.  The genomic landscape of pediatric renal cell carcinomas.

Authors:  Pengbo Beck; Barbara Selle; Lukas Madenach; David T W Jones; Christian Vokuhl; Apurva Gopisetty; Arash Nabbi; Ines B Brecht; Martin Ebinger; Jenny Wegert; Norbert Graf; Manfred Gessler; Stefan M Pfister; Natalie Jäger
Journal:  iScience       Date:  2022-03-26

Review 6.  MiTF/TFE Translocation Renal Cell Carcinomas: From Clinical Entities to Molecular Insights.

Authors:  Audrey Simonaggio; Damien Ambrosetti; Virginie Verkarre; Marie Auvray; Stéphane Oudard; Yann-Alexandre Vano
Journal:  Int J Mol Sci       Date:  2022-07-11       Impact factor: 6.208

7.  Prevalence and Landscape of Actionable Genomic Alterations in Renal Cell Carcinoma.

Authors:  Kyrollis Attalla; Renzo G DiNatale; Phillip M Rappold; Christopher J Fong; Francisco Sanchez-Vega; Andrew W Silagy; Stanley Weng; Jonathan Coleman; Chung-Han Lee; Maria I Carlo; Jeremy C Durack; Stephen B Solomon; Victor E Reuter; Paul Russo; Timothy A Chan; Robert J Motzer; Nikolaus D Schultz; Ed Reznik; Martin H Voss; A Ari Hakimi
Journal:  Clin Cancer Res       Date:  2021-07-14       Impact factor: 12.531
  7 in total

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