Genomic heterogeneity as a barrier to precision oncology in urothelial cancer

被引：32

作者：

Clinton, Timothy N. ^{[1
,10
]}

Chen, Ziyu ^{[2
]}

Wise, Hannah ^{[3
,11
]}

Lenis, Andrew T. ^{[1
]}

Chavan, Shweta ^{[4
]}

Donoghue, Mark T. A. ^{[4
]}

Almassi, Nima ^{[1
]}

Chu, Carissa E. ^{[1
]}

Dason, Shawn ^{[1
]}

Rao, Pavitra ^{[4
]}

Rodrigues, James A. ^{[5
]}

Vasani, Naresh B. ^{[5
]}

Ridouani, Fourat ^{[6
]}

Rosenberg, Jonathan E. ^{[7
]}

Bajorin, Dean F. ^{[7
]}

Teo, Min Yuen ^{[7
]}

Bochner, Bernard H. ^{[1
]}

Berger, Michael F. ^{[4
,8
]}

Ostrovnaya, Irina ^{[9
]}

Pietzak, Eugene J. ^{[1
]}

Iyer, Gopa ^{[7
]}

Gao, Sizhi Paul ^{[5
]}

Hu, Wenhuo ^{[5
]}

Al-Ahmadie, Hikmat A.

Solit, David B. ^{[4
,5
,7
]}

机构：

[1] Mem Sloan Kettering Canc Ctr, Dept Surg, Urol Serv, New York, NY 10065 USA

[2] Weill Cornell Med, Physiol Biophys & Syst Biol Program, New York, NY 10065 USA

[3] Mem Sloan Kettering Canc Ctr, Gerstner Sloan Kettering Grad Sch Biomed Sci, New York, NY 10065 USA

[4] Mem Sloan Kettering Canc Ctr, Marie Jose & Henry R Kravis Ctr Mol Oncol, New York, NY 10065 USA

[5] Mem Sloan Kettering Canc Ctr, Human Oncol & Pathogenesis Program, New York, NY 10065 USA

[6] Mem Sloan Kettering Canc Ctr, Dept Radiol, Intervent Radiol, New York, NY 10065 USA

[7] Mem Sloan Kettering Canc Ctr, Dept Med, Genitourinary Oncol Serv, New York, NY 10065 USA

[8] Mem Sloan Kettering Canc Ctr, Dept Pathol, New York, NY 10065 USA

[9] Mem Sloan Kettering Canc Ctr, Dept Epidemiol Biostat, New York, NY 10017 USA

[10] Brigham & Womens Hosp, Div Urol, Dept Surg, Boston, MA 02115 USA

[11] Flatiron Hlth, New York, NY 10013 USA

来源：

CELL REPORTS | 2022年 / 41卷 / 12期

关键词：

CLONAL EVOLUTION; ACQUIRED-RESISTANCE; MUTATION; INHIBITION; DISCOVERY; SELECTION; ALIGNMENT; BRAF;

D O I：

10.1016/j.celrep.2022.111859

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Precision oncology relies on the accurate molecular characterization of individual patients with cancer at the time of treatment initiation. However, tumor molecular profiles are not static, and cancers continually evolve because of ongoing mutagenesis and clonal selection. Here, we performed genomic analyses of primary tumors, metastases, and plasma collected from individual patients to define the concordance of actionable genomic alterations and to identify drivers of metastatic disease progression. We observed a high degree of discordance of actionable genomic alterations, with 23% discordant between primary and metastatic disease sites. Among chromatin-modifying genes, ARID1A mutations, when discordant, were exclusive to the metastatic tumor samples. Our findings indicate that the high degree of lesion-to-lesion genomic heterogeneity may be a barrier to precision oncology approaches for bladder cancer and that circulating tumor DNA profiling may be preferred to tumor sequencing for a subset of patients.

引用

页数：15

共 55 条

[1] Signatures of mutational processes in human cancer [J].

Alexandrov, Ludmil B. ;

Nik-Zainal, Serena ;

Wedge, David C. ;

Aparicio, Samuel A. J. R. ;

Behjati, Sam ;

Biankin, Andrew V. ;

Bignell, Graham R. ;

Bolli, Niccolo ;

Borg, Ake ;

Borresen-Dale, Anne-Lise ;

Boyault, Sandrine ;

Burkhardt, Birgit ;

Butler, Adam P. ;

Caldas, Carlos ;

Davies, Helen R. ;

Desmedt, Christine ;

Eils, Roland ;

Eyfjord, Jorunn Erla ;

Foekens, John A. ;

Greaves, Mel ;

Hosoda, Fumie ;

Hutter, Barbara ;

Ilicic, Tomislav ;

Imbeaud, Sandrine ;

Imielinsk, Marcin ;

Jaeger, Natalie ;

Jones, David T. W. ;

Jones, David ;

Knappskog, Stian ;

Kool, Marcel ;

Lakhani, Sunil R. ;

Lopez-Otin, Carlos ;

Martin, Sancha ;

Munshi, Nikhil C. ;

Nakamura, Hiromi ;

Northcott, Paul A. ;

Pajic, Marina ;

Papaemmanuil, Elli ;

Paradiso, Angelo ;

Pearson, John V. ;

Puente, Xose S. ;

Raine, Keiran ;

Ramakrishna, Manasa ;

Richardson, Andrea L. ;

Richter, Julia ;

Rosenstiel, Philip ;

Schlesner, Matthias ;

Schumacher, Ton N. ;

Span, Paul N. ;

Teague, Jon W. .

NATURE, 2013, 500 (7463) :415-+

[2]

Benjamin DI, 2019, bioRxiv, DOI [10.1101/861054, 10.1101/861054, DOI 10.1101/861054]

[3] Genome doubling shapes the evolution and prognosis of advanced cancers [J].

Bielski, Craig M. ;

Zehir, Ahmet ;

Penson, Alexander V. ;

Donoghue, Mark T. A. ;

Chatila, Walid ;

Armenia, Joshua ;

Chang, Matthew T. ;

Schram, Alison M. ;

Jonsson, Philip ;

Bandlamudi, Chaitanya ;

Razavi, Pedram ;

Iyer, Gopa ;

Robson, Mark E. ;

Stadler, Zsofia K. ;

Schultz, Nikolaus ;

Baselga, Jose ;

Solit, David B. ;

Hyman, David M. ;

Berger, Michael F. ;

Taylor, Barry S. .

NATURE GENETICS, 2018, 50 (08) :1189-+

[4] MUTATION SELECTION AND NATURAL-HISTORY OF CANCER [J].

CAIRNS, J .

NATURE, 1975, 255 (5505) :197-200

[5] The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data [J].

Cerami, Ethan ;

Gao, Jianjiong ;

Dogrusoz, Ugur ;

Gross, Benjamin E. ;

Sumer, Selcuk Onur ;

Aksoy, Buelent Arman ;

Jacobsen, Anders ;

Byrne, Caitlin J. ;

Heuer, Michael L. ;

Larsson, Erik ;

Antipin, Yevgeniy ;

Reva, Boris ;

Goldberg, Arthur P. ;

Sander, Chris ;

Schultz, Nikolaus .

CANCER DISCOVERY, 2012, 2 (05) :401-404

[6]

Chakravarty Debyani, 2017, JCO Precis Oncol, V2017, DOI 10.1200/PO.17.00011

[7] Small-Cell Carcinomas of the Bladder and Lung Are Characterized by a Convergent but Distinct Pathogenesis [J].

Chang, Matthew T. ;

Penson, Alexander ;

Desai, Neil B. ;

Socci, Nicholas D. ;

Shen, Ronglai ;

Seshan, Venkatraman E. ;

Kundra, Ritika ;

Abeshouse, Adam ;

Viale, Agnes ;

Cha, Eugene K. ;

Hao, Xueli ;

Reuter, Victor E. ;

Rudin, Charles M. ;

Bochner, Bernard H. ;

Rosenberg, Jonathan E. ;

Bajorin, Dean F. ;

Schultz, Nikolaus ;

Berger, Michael F. ;

Iyer, Gopa ;

Solit, David B. ;

Al-Ahmadie, Hikmat A. ;

Taylor, Barry S. .

CLINICAL CANCER RESEARCH, 2018, 24 (08) :1965-1973

[8] Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications [J].

Chen, Xiaoyu ;

Schulz-Trieglaff, Ole ;

Shaw, Richard ;

Barnes, Bret ;

Schlesinger, Felix ;

Kallberg, Morten ;

Cox, Anthony J. ;

Kruglyakl, Semyon ;

Saunders, Christopher T. .

BIOINFORMATICS, 2016, 32 (08) :1220-1222

[9] Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology [J].

Cheng, Donavan T. ;

Mitchell, Talia N. ;

Zehir, Ahmet ;

Shah, Ronak H. ;

Benayed, Ryma ;

Syed, Aijazuddin ;

Chandramohan, Raghu ;

Liu, Zhen Yu ;

Won, Helen H. ;

Scott, Sasinya N. ;

Brannon, A. Rose ;

O'Reilly, Catherine ;

Sadowska, Justyna ;

Casanova, Jacklyn ;

Yannes, Angela ;

Hechtman, Jaclyn F. ;

Yao, Jinjuan ;

Song, Wei ;

Ross, Dara S. ;

Oultache, Alifya ;

Dogan, Snjezana ;

Borsu, Laetitia ;

Hameed, Meera ;

Nafa, Khedoudja ;

Arcila, Maria E. ;

Ladanyi, Marc ;

Berger, Michael F. .

JOURNAL OF MOLECULAR DIAGNOSTICS, 2015, 17 (03) :251-264

[10] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

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