1
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Schlabach MR, Lin S, Collester ZR, Wrocklage C, Shenker S, Calnan C, Xu T, Gannon HS, Williams LJ, Thompson F, Dunbar PR, LaMothe RA, Garrett TE, Colletti N, Hohmann AF, Tubo NJ, Bullock CP, Le Mercier I, Sofjan K, Merkin JJ, Keegan S, Kryukov GV, Dugopolski C, Stegmeier F, Wong K, Sharp FA, Cadzow L, Benson MJ. Rational design of a SOCS1-edited tumor-infiltrating lymphocyte therapy using CRISPR/Cas9 screens. J Clin Invest 2023; 133:e163096. [PMID: 38099496 PMCID: PMC10721144 DOI: 10.1172/jci163096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/10/2023] [Indexed: 12/18/2023] Open
Abstract
Cell therapies such as tumor-infiltrating lymphocyte (TIL) therapy have shown promise in the treatment of patients with refractory solid tumors, with improvement in response rates and durability of responses nevertheless sought. To identify targets capable of enhancing the antitumor activity of T cell therapies, large-scale in vitro and in vivo clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 screens were performed, with the SOCS1 gene identified as a top T cell-enhancing target. In murine CD8+ T cell-therapy models, SOCS1 served as a critical checkpoint in restraining the accumulation of central memory T cells in lymphoid organs as well as intermediate (Texint) and effector (Texeff) exhausted T cell subsets derived from progenitor exhausted T cells (Texprog) in tumors. A comprehensive CRISPR tiling screen of the SOCS1-coding region identified sgRNAs targeting the SH2 domain of SOCS1 as the most potent, with an sgRNA with minimal off-target cut sites used to manufacture KSQ-001, an engineered TIL therapy with SOCS1 inactivated by CRISPR/Cas9. KSQ-001 possessed increased responsiveness to cytokine signals and enhanced in vivo antitumor function in mouse models. These data demonstrate the use of CRISPR/Cas9 screens in the rational design of T cell therapies.
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2
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Buckbinder L, St. Jean DJ, Tieu T, Ladd B, Hilbert B, Wang W, Alltucker JT, Manimala S, Kryukov GV, Brooijmans N, Dowdell G, Jonsson P, Huff M, Guzman-Perez A, Jackson EL, Goncalves MD, Stuart DD. STX-478, a Mutant-Selective, Allosteric PI3Kα Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Kα-Mutant Xenografts. Cancer Discov 2023; 13:2432-2447. [PMID: 37623743 PMCID: PMC10618743 DOI: 10.1158/2159-8290.cd-23-0396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/24/2023] [Accepted: 08/23/2023] [Indexed: 08/26/2023]
Abstract
Phosphoinositide 3-kinase α (PIK3CA) is one of the most mutated genes across cancers, especially breast, gynecologic, and head and neck squamous cell carcinoma tumors. Mutations occur throughout the gene, but hotspot mutations in the helical and kinase domains predominate. The therapeutic benefit of isoform-selective PI3Kα inhibition was established with alpelisib, which displays equipotent activity against the wild-type and mutant enzyme. Inhibition of wild-type PI3Kα is associated with severe hyperglycemia and rash, which limits alpelisib use and suggests that selectively targeting mutant PI3Kα could reduce toxicity and improve efficacy. Here we describe STX-478, an allosteric PI3Kα inhibitor that selectively targets prevalent PI3Kα helical- and kinase-domain mutant tumors. STX-478 demonstrated robust efficacy in human tumor xenografts without causing the metabolic dysfunction observed with alpelisib. Combining STX-478 with fulvestrant and/or cyclin-dependent kinase 4/6 inhibitors was well tolerated and provided robust and durable tumor regression in ER+HER2- xenograft tumor models. SIGNIFICANCE These preclinical data demonstrate that the mutant-selective, allosteric PI3Kα inhibitor STX-478 provides robust efficacy while avoiding the metabolic dysfunction associated with the nonselective inhibitor alpelisib. Our results support the ongoing clinical evaluation of STX-478 in PI3Kα-mutated cancers, which is expected to expand the therapeutic window and mitigate counterregulatory insulin release. See related commentary by Kearney and Vasan, p. 2313. This article is featured in Selected Articles from This Issue, p. 2293.
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Affiliation(s)
| | - David J. St. Jean
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Trang Tieu
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Brendon Ladd
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Brendan Hilbert
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Weixue Wang
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | | | - Samantha Manimala
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | | | | | - Gregory Dowdell
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Philip Jonsson
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | - Michael Huff
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
| | | | - Erica L. Jackson
- Department of Biology, Scorpion Therapeutics, South San Francisco, California
| | - Marcus D. Goncalves
- Division of Endocrinology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Darrin D. Stuart
- Research and Development, Scorpion Therapeutics, Boston, Massachusetts
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3
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Stuart DD, Guzman-Perez A, Brooijmans N, Jackson EL, Kryukov GV, Friedman AA, Hoos A. Precision Oncology Comes of Age: Designing Best-in-Class Small Molecules by Integrating Two Decades of Advances in Chemistry, Target Biology, and Data Science. Cancer Discov 2023; 13:2131-2149. [PMID: 37712571 PMCID: PMC10551669 DOI: 10.1158/2159-8290.cd-23-0280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Small-molecule drugs have enabled the practice of precision oncology for genetically defined patient populations since the first approval of imatinib in 2001. Scientific and technology advances over this 20-year period have driven the evolution of cancer biology, medicinal chemistry, and data science. Collectively, these advances provide tools to more consistently design best-in-class small-molecule drugs against known, previously undruggable, and novel cancer targets. The integration of these tools and their customization in the hands of skilled drug hunters will be necessary to enable the discovery of transformational therapies for patients across a wider spectrum of cancers. SIGNIFICANCE Target-centric small-molecule drug discovery necessitates the consideration of multiple approaches to identify chemical matter that can be optimized into drug candidates. To do this successfully and consistently, drug hunters require a comprehensive toolbox to avoid following the "law of instrument" or Maslow's hammer concept where only one tool is applied regardless of the requirements of the task. Combining our ever-increasing understanding of cancer and cancer targets with the technological advances in drug discovery described below will accelerate the next generation of small-molecule drugs in oncology.
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Affiliation(s)
| | | | | | | | | | | | - Axel Hoos
- Scorpion Therapeutics, Boston, Massachusetts
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4
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Stover EH, Oh C, Keskula P, Choudhury AD, Tseng YY, Adalsteinsson VA, Lohr JG, Thorner AR, Ducar M, Kryukov GV, Ha G, Rosenberg M, Freeman SS, Zhang Z, Wu X, Van Allen EM, Takeda DY, Loda M, Wu CL, Taplin ME, Garraway LA, Boehm JS, Huang FW. Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate 2022; 82:584-597. [PMID: 35084050 PMCID: PMC8887817 DOI: 10.1002/pros.24305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Primary and metastatic prostate cancers have low mutation rates and recurrent alterations in a small set of genes, enabling targeted sequencing of prostate cancer-associated genes as an efficient approach to characterizing patient samples (compared to whole-exome and whole-genome sequencing). For example, targeted sequencing provides a flexible, rapid, and cost-effective method for genomic assessment of patient-derived cell lines to evaluate fidelity to initial patient tumor samples. METHODS We developed a prostate cancer-specific targeted next-generation sequencing (NGS) panel to detect alterations in 62 prostate cancer-associated genes as well as recurring gene fusions with ETS family members, representing the majority of common alterations in prostate cancer. We tested this panel on primary prostate cancer tissues and blood biopsies from patients with metastatic prostate cancer. We generated patient-derived cell lines from primary prostate cancers using conditional reprogramming methods and applied targeted sequencing to evaluate the fidelity of these cell lines to the original patient tumors. RESULTS The prostate cancer-specific panel identified biologically and clinically relevant alterations, including point mutations in driver oncogenes and ETS family fusion genes, in tumor tissues from 29 radical prostatectomy samples. The targeted panel also identified genomic alterations in cell-free DNA and circulating tumor cells (CTCs) from patients with metastatic prostate cancer, and in standard prostate cancer cell lines. We used the targeted panel to sequence our set of patient-derived cell lines; however, no prostate cancer-specific mutations were identified in the tumor-derived cell lines, suggesting preferential outgrowth of normal prostate epithelial cells. CONCLUSIONS We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.
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Affiliation(s)
- Elizabeth H. Stover
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Coyin Oh
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Jens G. Lohr
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Gregory V. Kryukov
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Gavin Ha
- Fred Hutchinson Cancer Research Center, Seattle WA
| | | | | | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston MA
- University of Massachusetts Memorial Medical Center, Worcester MA
| | | | - Eliezer M. Van Allen
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Massimo Loda
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY
| | - Chin-Lee Wu
- Harvard Medical School, Boston MA
- Massachusetts General Hospital, Boston MA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
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5
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Li H, Ning S, Ghandi M, Kryukov GV, Gopal S, Deik A, Souza A, Pierce K, Keskula P, Hernandez D, Ann J, Shkoza D, Apfel V, Zou Y, Vazquez F, Barretina J, Pagliarini RA, Galli GG, Root DE, Hahn WC, Tsherniak A, Giannakis M, Schreiber SL, Clish CB, Garraway LA, Sellers WR. The landscape of cancer cell line metabolism. Nat Med 2019; 25:850-860. [PMID: 31068703 PMCID: PMC6629041 DOI: 10.1038/s41591-019-0404-8] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/20/2019] [Indexed: 02/08/2023]
Abstract
Despite considerable efforts to identify cancer metabolic alterations that might unveil druggable vulnerabilities, systematic characterizations of metabolism as it relates to functional genomic features and associated dependencies remain uncommon. To further understand the metabolic diversity of cancer, we profiled 225 metabolites in 928 cell lines from more than 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) using liquid chromatography-mass spectrometry (LC-MS). This resource enables unbiased association analysis linking the cancer metabolome to genetic alterations, epigenetic features and gene dependencies. Additionally, by screening barcoded cell lines, we demonstrated that aberrant ASNS hypermethylation sensitizes subsets of gastric and hepatic cancers to asparaginase therapy. Finally, our analysis revealed distinct synthesis and secretion patterns of kynurenine, an immune-suppressive metabolite, in model cancer cell lines. Together, these findings and related methodology provide comprehensive resources that will help clarify the landscape of cancer metabolism.
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Affiliation(s)
- Haoxin Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaoyang Ning
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | | | | | - Shuba Gopal
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amy Deik
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amanda Souza
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kerry Pierce
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Julie Ann
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Dojna Shkoza
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Verena Apfel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Yilong Zou
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jordi Barretina
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Giorgio G Galli
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Marios Giannakis
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2018; 565:E5-E6. [PMID: 30559381 DOI: 10.1038/s41586-018-0722-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam A Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Sage Bionetworks, 1100 Fairview Ave. N., Seattle, Washington, 98109, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Christopher J Wilson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Gregory V Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael F Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - John E Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Felipa A Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Ingo H Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Guoying K Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Robert C Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill P Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Barbara L Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jennifer L Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Todd R Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Michael P Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA.
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA. .,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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7
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Janouskova H, El Tekle G, Bellini E, Udeshi ND, Rinaldi A, Ulbricht A, Bernasocchi T, Civenni G, Losa M, Svinkina T, Bielski CM, Kryukov GV, Cascione L, Napoli S, Enchev RI, Mutch DG, Carney ME, Berchuck A, Winterhoff BJN, Broaddus RR, Schraml P, Moch H, Bertoni F, Catapano CV, Peter M, Carr SA, Garraway LA, Wild PJ, Theurillat JPP. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med 2017; 23:1046-1054. [PMID: 28805821 PMCID: PMC5592092 DOI: 10.1038/nm.4372] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations in the substrate recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancer. Their therapeutic implications remain incompletely understood. Here, we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutants impaired degradation of BETs, promoting resistance against their pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations within the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat endometrial but not prostate cancer patients with SPOP mutations.
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Affiliation(s)
- Hana Janouskova
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Geniver El Tekle
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elisa Bellini
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Namrata D Udeshi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anna Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Anna Ulbricht
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Tiziano Bernasocchi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Gianluca Civenni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Marco Losa
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Tanya Svinkina
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Craig M Bielski
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Luciano Cascione
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Radoslav I Enchev
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - David G Mutch
- Division of Gynecologic Oncology, Washington University, St. Louis, Missouri, USA
| | - Michael E Carney
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke Cancer Center, Durham, North Carolina, USA
| | - Boris J N Winterhoff
- Division of Gynecologic Oncology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Russell R Broaddus
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Matthias Peter
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Steven A Carr
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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8
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Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. Selenoprotein Gene Nomenclature. J Biol Chem 2016; 291:24036-24040. [PMID: 27645994 DOI: 10.1074/jbc.m116.756155] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.
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Affiliation(s)
- Vadim N Gladyshev
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, .,the Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
| | - Elias S Arnér
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Marla J Berry
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | | | - Elspeth A Bruford
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Raymond F Burk
- the Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Bradley A Carlson
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Sergi Castellano
- the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurent Chavatte
- the Centre International de Recherche en Infectiologie, CIRI, INSERM U1111, and CNRS/ENS UMR5308, 69007 Lyon, France
| | - Marcus Conrad
- the Helmholtz Zentrum München, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Paul R Copeland
- the Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Alan M Diamond
- the Department of Pathology, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Donna M Driscoll
- the Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Ana Ferreiro
- the Pathophysiology of Striated Muscles Laboratory, Unit of Functional and Adaptive Biology (BFA), University Paris Diderot, Sorbonne Paris Cité, BFA, UMR CNRS 8251, 75250 Paris, France.,the AP-HP, Centre de Référence Maladies Neuromusculaires Paris-Est, Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Leopold Flohé
- the Universidad de la República, Facultad de Medicina, Departamento de Bioquímica, 11800 Montevideo, Uruguay.,the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Fiona R Green
- the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Roderic Guigó
- the Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.,the Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Diane E Handy
- the Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Dolph L Hatfield
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - John Hesketh
- the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the The Medical School, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Peter R Hoffmann
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | - Arne Holmgren
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Robert J Hondal
- the Department of Biochemistry, University of Vermont, Burlington, Vermont 05405
| | - Michael T Howard
- the Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Kaixun Huang
- the Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China
| | - Hwa-Young Kim
- the Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 42415, South Korea
| | - Ick Young Kim
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Josef Köhrle
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Alain Krol
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | | | - Byeong Jae Lee
- the School of Biological Sciences, Seoul National University, Seoul 151-742, South Korea
| | - Byung Cheon Lee
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Xin Gen Lei
- the Department of Animal Science, Cornell University, Ithaca, New York 14853
| | - Qiong Liu
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
| | - Alain Lescure
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France.,the Centre National de la Recherche Scientifique, 75794 Paris, France
| | - Alexei V Lobanov
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Joseph Loscalzo
- the Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Matilde Maiorino
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Marco Mariotti
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - K Sandeep Prabhu
- the Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Margaret P Rayman
- the Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Sharon Rozovsky
- the Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Gustavo Salinas
- the Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, CP11600 Montevideo, Uruguay
| | - Edward E Schmidt
- the Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Lutz Schomburg
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Ulrich Schweizer
- the Rheinische Friedrich-Wilhelms Universität Bonn, Institut für Biochemie und Molekularbiologie, 53115 Bonn, Germany
| | - Miljan Simonović
- the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Roger A Sunde
- the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Petra A Tsuji
- the Department of Biological Sciences, Towson University, Towson, Maryland 21252, and
| | - Susan Tweedie
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Fulvio Ursini
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Philip D Whanger
- the Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, Oregon 97331
| | - Yan Zhang
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
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9
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Tseng YY, Keskula P, Hong AL, Gill S, Cheah JH, Kryukov GV, Tsherniak A, Vazquez F, Cowley G, Oh C, Peng A, Sayeed A, Deasy R, Ronning P, Kantoff P, Garraway L, Rubin MA, Kuo C, Puram S, Gazdar A, Cruz FSD, Bass A, Wagle N, Ligon KL, Janeway K, Root D, Schreiber SL, Clemons PA, Shamji A, Hahn WC, Golub TR, Boehm JS. Abstract B26: Accelerating prediction of tumor vulnerabilities using next-generation cancer models. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.pdx16-b26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The development of new cancer therapeutics requires sufficient genetic and phenotypic diversity of cancer models. Current collections of human cancer cell lines are limited and for many rare cancer types, zero models exist that are broadly available. Here, we report results from the pilot phase of the Cancer Cell Line Factory (CCLF) project that aims to overcome this obstacle by systematically creating next-generation in vitro cancer models from adult and pediatric cancer patients' specimens and making these models broadly available.
We first developed a workflow of laboratory, genomics and informatics tools that make it possible to systematically compare published ex vivo culture conditions for each individual tumor to enable the scientific community to iterate towards disease-specific culture recipes. Based on sample volume and rarity, 4-100 conditions were applied to each sample and all data was captured in a custom Laboratory Information Management System to enhance subsequent predictions. We developed a $150, 5-day turnaround genomics panel to validate cultures based on genomics. Importantly, we show that tumor genomics can be retained in such patient-derived models and tumor genomics are generally stable across 20 passages. Since the inception of this project, we have processed over 650 patient cancer specimens from 450 patients across 16 tumor types and report the successful generation of over 100 genomically characterized adult and pediatric cancer and normal models.
We next hypothesized that novel patient-derived cultures could be used to enhance dependency predictions. To do so, we tested 65 cell lines against the “informer” set of 440 compounds developed by the Broad Cancer Target Discovery and Development (CTD2) Center. We show that generating cell lines and testing their sensitivities within 3 months is feasible and the drug responses are reproducible. Moreover, to strengthen relationships between drug sensitivities and cellular features, we compared results with recently published data on the identical compounds tested against 860 existing cell lines. With this approach, we are able to identify many known drug dependencies in these novel models and exhibit the consistency sensitivities compared to existing cell lines. We are also evaluating drug sensitivity predictors for novel dependencies. Overall, our proof-of-concept framework demonstrates initial feasibility of rapidly generating cancer models and assessing drug sensitivities at scale.
Citation Format: Yuen-Yi Tseng, Paula Keskula, Andrew L. Hong, Shubhroz Gill, Jaime H. Cheah, Gregory V. Kryukov, Aviad Tsherniak, Francisca Vazquez, Glenn Cowley, Coyin Oh, Anson Peng, Abeer Sayeed, Rebecca Deasy, Peter Ronning, Philip Kantoff, Levi Garraway, Mark A. Rubin, Calvin Kuo, Sidharth Puram, Adi Gazdar, Filemon S. Dela Cruz, Jr., Adam Bass, Jr., Nikhil Wagle, Keith L. Ligon, Katherine Janeway, David Root, Stuart L. Schreiber, Paul A. Clemons, Aly Shamji, William C. Hahn, Todd R. Golub, Jesse S. Boehm. Accelerating prediction of tumor vulnerabilities using next-generation cancer models. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B26.
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Affiliation(s)
- Yuen-Yi Tseng
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Paula Keskula
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Shubhroz Gill
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Jaime H. Cheah
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | | | | | | | - Glenn Cowley
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Coyin Oh
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Anson Peng
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Abeer Sayeed
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Rebecca Deasy
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | - Peter Ronning
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | - Adi Gazdar
- 7University of Texas Southwestern Medical Center, Dallas, TX,
| | | | - Adam Bass
- 2Dana-Farber Cancer Institute, Boston, MA,
| | | | | | | | - David Root
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | - Aly Shamji
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Todd R. Golub
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
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10
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Podolskiy DI, Lobanov AV, Kryukov GV, Gladyshev VN. Analysis of cancer genomes reveals basic features of human aging and its role in cancer development. Nat Commun 2016; 7:12157. [PMID: 27515585 PMCID: PMC4990632 DOI: 10.1038/ncomms12157] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/07/2016] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations have long been implicated in aging and disease, but their impact on fitness and function is difficult to assess. Here by analysing human cancer genomes we identify mutational patterns associated with aging. Our analyses suggest that age-associated mutation load and burden double approximately every 8 years, similar to the all-cause mortality doubling time. This analysis further reveals variance in the rate of aging among different human tissues, for example, slightly accelerated aging of the reproductive system. Age-adjusted mutation load and burden correlate with the corresponding cancer incidence and precede it on average by 15 years, pointing to pre-clinical cancer development times. Behaviour of mutation load also exhibits gender differences and late-life reversals, explaining some gender-specific and late-life patterns in cancer incidence rates. Overall, this study characterizes some features of human aging and offers a mechanism for age being a risk factor for the onset of cancer. Somatic mutations are associated with disease, including cancer. Here, the authors analyse cancer genomic data and show that somatic mutations increase with age and that cancer incidence lags 15 years behind this increase, later in life, mutation and cancer incidence are reduced.
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Affiliation(s)
- Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute, Cambridge, Massachusetts 02142, USA
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11
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Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CWM, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS. Integrated genetic and pharmacologic interrogation of rare cancers. Nat Commun 2016; 7:11987. [PMID: 27329820 PMCID: PMC4917959 DOI: 10.1038/ncomms11987] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
Identifying therapeutic targets in rare cancers remains challenging due to the paucity of established models to perform preclinical studies. As a proof-of-concept, we developed a patient-derived cancer cell line, CLF-PED-015-T, from a paediatric patient with a rare undifferentiated sarcoma. Here, we confirm that this cell line recapitulates the histology and harbours the majority of the somatic genetic alterations found in a metastatic lesion isolated at first relapse. We then perform pooled CRISPR-Cas9 and RNAi loss-of-function screens and a small-molecule screen focused on druggable cancer targets. Integrating these three complementary and orthogonal methods, we identify CDK4 and XPO1 as potential therapeutic targets in this cancer, which has no known alterations in these genes. These observations establish an approach that integrates new patient-derived models, functional genomics and chemical screens to facilitate the discovery of targets in rare cancers.
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Affiliation(s)
- Andrew L. Hong
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Glenn S. Cowley
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Oliver Jonas
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Jaime H. Cheah
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Bryan D. Kynnap
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Mihir B. Doshi
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Coyin Oh
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Stephanie C. Meyer
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alanna J. Church
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Shubhroz Gill
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Craig M. Bielski
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paula Keskula
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alma Imamovic
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Sara Howell
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Gregory V. Kryukov
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Paul A. Clemons
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Brian D. Crompton
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Alykhan F. Shamji
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Carlos Rodriguez-Galindo
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Katherine A. Janeway
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Charles W. M. Roberts
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Kimberly Stegmaier
- Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paul van Hummelen
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Michael J. Cima
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Robert S. Langer
- Koch Institute for Integrative Cancer Research at MIT, 500 Main Street, Cambridge, Massachusetts 02139, USA
| | - Levi A. Garraway
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Stuart L. Schreiber
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David E. Root
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - William C. Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
- Brigham and Women's Hospital, 75 Francis Street, Boston, Massachusetts 02115, USA
| | - Jesse S. Boehm
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA
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12
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Hong AL, Cowley GS, Tseng YY, Cheah JH, Jonas O, Doshi MB, Kynnap BD, Oh C, Meyer S, Clemons P, Burger M, Vazquez F, Weir B, Kryukov GV, Church A, Imamovic A, Tsherniak A, Bielski C, Crompton B, Mullen E, Roberts C, Rodriguez-Galindo C, Janeway KA, Stegmaier K, Hummelen PV, Langer R, Garraway LA, Schreiber SL, Root DE, Boehm JS, Hahn WC. Abstract B38: Developing a functional genomics platform to interrogate rare pediatric cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.pedca15-b38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Of pediatric solid tumors, as many as 10% of tumors are categorized as rare. Many of these rare tumors lack standard effective known therapy. The ability to identify vulnerabilities for many rare tumors has been significantly limited by the lack of in vitro and in vivo models. Furthermore, current approaches to study such vulnerabilities are usually limited to a specific compound or target. Our objectives were 1) to develop a platform to collect tumor samples and generate in vitro models and 2) to develop systematic and orthogonal approaches focused on currently known druggable cancer targets to identify vulnerabilities in these difficult to treat cancers. We have developed a proof of concept cell line from a patient who succumbed to progressive undifferentiated sarcoma treated on an aggressive multi-therapy regimen. This cell line, in its early passages, has novel gene fusions that match that of the primary tumor. Furthermore, even at early passages, this cell line was amenable to high throughput functional screens. Using a targeted pooled shRNA screen (employing matched seed controls) and an analogous CRISPR screen we identified dependencies to XPO1 and CDK4. In parallel, compounds against these targets were identified in a small molecule compound screen. These targetable dependencies were further validated in vivo with a micro-dosing device. These observations identify new targets in this rare malignancy. Furthermore, this suggests that the interrogation of patient derived cell lines facilitates the identification of testable therapeutic approaches.
Citation Format: Andrew L. Hong, Glenn S. Cowley, Yuen-Yi Tseng, Jaime H. Cheah, Oliver Jonas, Mihir B. Doshi, Bryan D. Kynnap, Coyin Oh, Stephanie Meyer, Paul Clemons, Michael Burger, Francisca Vazquez, Barbara Weir, Gregory V. Kryukov, Alanna Church, Alma Imamovic, Aviad Tsherniak, Craig Bielski, Brian Crompton, Elizabeth Mullen, Charles Roberts, Carlos Rodriguez-Galindo, Katherine A. Janeway, Kimberly Stegmaier, Paul van Hummelen, Robert Langer, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Jesse S. Boehm, William C. Hahn. Developing a functional genomics platform to interrogate rare pediatric cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B38.
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Affiliation(s)
| | | | | | - Jaime H. Cheah
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | - Oliver Jonas
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
| | | | | | - Coyin Oh
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | - Paul Clemons
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | - Barbara Weir
- 2Broad Institute of Harvard and MIT, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | - Robert Langer
- 3Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA,
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13
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Kryukov GV, Wilson FH, Ruth JR, Paulk J, Tsherniak A, Marlow SE, Vazquez F, Weir BA, Fitzgerald ME, Tanaka M, Bielski CM, Scott JM, Dennis C, Cowley GS, Boehm JS, Root DE, Golub TR, Clish CB, Bradner JE, Hahn WC, Garraway LA. MTAP deletion confers enhanced dependency on the PRMT5 arginine methyltransferase in cancer cells. Science 2016; 351:1214-8. [PMID: 26912360 DOI: 10.1126/science.aad5214] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/01/2016] [Indexed: 12/19/2022]
Abstract
The discovery of cancer dependencies has the potential to inform therapeutic strategies and to identify putative drug targets. Integrating data from comprehensive genomic profiling of cancer cell lines and from functional characterization of cancer cell dependencies, we discovered that loss of the enzyme methylthioadenosine phosphorylase (MTAP) confers a selective dependence on protein arginine methyltransferase 5 (PRMT5) and its binding partner WDR77. MTAP is frequently lost due to its proximity to the commonly deleted tumor suppressor gene, CDKN2A. We observed increased intracellular concentrations of methylthioadenosine (MTA, the metabolite cleaved by MTAP) in cells harboring MTAP deletions. Furthermore, MTA specifically inhibited PRMT5 enzymatic activity. Administration of either MTA or a small-molecule PRMT5 inhibitor showed a modest preferential impairment of cell viability for MTAP-null cancer cell lines compared with isogenic MTAP-expressing counterparts. Together, our findings reveal PRMT5 as a potential vulnerability across multiple cancer lineages augmented by a common "passenger" genomic alteration.
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Affiliation(s)
- Gregory V Kryukov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frederick H Wilson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason R Ruth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviad Tsherniak
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sara E Marlow
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Francisca Vazquez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Barbara A Weir
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Minoru Tanaka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Craig M Bielski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin M Scott
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Courtney Dennis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Glenn S Cowley
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse S Boehm
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Huang FW, Bielski CM, Rinne ML, Hahn WC, Sellers WR, Stegmeier F, Garraway LA, Kryukov GV. TERT promoter mutations and monoallelic activation of TERT in cancer. Oncogenesis 2015; 4:e176. [PMID: 26657580 PMCID: PMC4688396 DOI: 10.1038/oncsis.2015.39] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/15/2022] Open
Abstract
Here we report that promoter mutations in telomerase (TERT), the most common noncoding mutations in cancer, give rise to monoallelic expression of TERT. Through deep RNA sequencing, we find that TERT activation in human cancer cell lines can occur in either mono- or biallelic manner. Without exception, hotspot TERT promoter mutations lead to the re-expression of only one allele, accounting for approximately half of the observed cases of monoallelic TERT expression. Furthermore, we show that monoallelic TERT expression is highly prevalent in certain tumor types and widespread across a broad spectrum of cancers. Taken together, these observations provide insights into the mechanisms of TERT activation and the ramifications of noncoding mutations in cancer.
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Affiliation(s)
- F W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - C M Bielski
- Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - M L Rinne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - W C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - W R Sellers
- Oncology Disease Area, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - F Stegmeier
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - L A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - G V Kryukov
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
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Kryukov GV, Bielski CM, Samocha K, Fromer M, Seepo S, Gentry C, Neale B, Garraway LA, Sweeney CJ, Taplin ME, Van Allen EM. Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors. Clin Cancer Res 2015; 22:2183-9. [PMID: 26631610 DOI: 10.1158/1078-0432.ccr-15-2317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/09/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancer survivors express anxiety that chemotherapy exposure may lead to transmissible genetic damage in posttreatment children. Preclinical models suggest that chemotherapy exposure may result in considerable genomic alterations in postexposure progeny. Epidemiologic studies have not demonstrated a significant increase in congenital abnormalities in posttreatment children of cancer survivors, but the inherited genome-wide effect of chemotherapy exposure in humans is unknown. EXPERIMENTAL DESIGN Two testicular cancer survivors cured with chemotherapy who had children pre- and postexposure without sperm banking were identified. Familial germline whole genome sequencing (WGS) was performed for these families, and analytic methods were utilized to identify de novo alterations, including mutations, recombinations, and structural rearrangements in the pre- and postexposure offspring. RESULTS No increase in de novo germline mutations in postexposure children compared with their preexposure siblings was found. Furthermore, there were no increased short insertion/deletions, recombination frequency, or structural rearrangements in these postexposure children. CONCLUSIONS In two families of male cancer survivors, there was no transmissible genomic impact of significant mutagenic exposure in postexposure children. This study may provide possible reassuring evidence for patients undergoing chemotherapy who are unable to have pretreatment sperm cryopreservation. Expanded cohorts that utilize WGS to identify environmental exposure effects on the inherited genome may inform the generalizability of these results. Clin Cancer Res; 22(9); 2183-9. ©2015 AACR.
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Affiliation(s)
- Gregory V Kryukov
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Craig M Bielski
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kaitlin Samocha
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Menachem Fromer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York. Department of Psychiatry, Mount Sinai School of Medicine, New York, New York
| | - Sara Seepo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Carleen Gentry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Benjamin Neale
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Eliezer M Van Allen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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Chan HM, Jaffe JD, Wang Y, Zhang J, Huether R, Kryukov GV, Bhang HEC, Taylor JE, Hu M, Englund NP, Yan F, Wang Z, McDonald ER, Wei L, Ma J, Easton J, Yu Z, deBeaumount R, Gibaja V, Venkatesan K, Schlegel R, Sellers WR, Keen N, Liu J, Caponigro G, Barretina J, Cooke VG, Mullighan C, Carr SA, Downing JR, Garraway LA, Stegmeier F. Abstract 2930: Global chromatin profiling reveals NSD2 mutation in pediatric ALL. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-2930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic dysregulation is an emerging hallmark of cancers. We developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancers. When applied to 115 lines of the Cancer Cell Line Encyclopedia1, this approach identified distinct molecular chromatin signatures. One signature was characterized by increased H3K36 dimethylation, exhibited by several lines harboring NSD2 translocations. A novel NSD2 p.E1099K variant was identified in non-translocated acute lymphoblastic leukemia (ALL) lines sharing this signature. Ectopic expression of the variant induced a chromatin signature characteristic of NSD2 hyperactivation and promoted transformation. NSD2 knockdown selectively inhibited the proliferation of NSD2-mutant lines and impaired the in vivo growth of an NSD2-mutant ALL xenograft. Sequencing analysis of >1000 pediatric cancer genomes identified the NSD2 p.E1099K mutation in 14% of t(12;21)[ETV6-RUNX1]-containing ALLs. These findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes.
1.
Barretina,J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
Citation Format: Ho Man Chan, Jacob D. Jaffe, Yan Wang, Jinghui Zhang, Robert Huether, Gregory V. Kryukov, Hyo-eun C. Bhang, Jordan E. Taylor, Min Hu, Nathan P. Englund, Feng Yan, Zhaofu Wang, E Robert McDonald III, Lei Wei, Jing Ma, John Easton, Zhengtian Yu, Rosalie deBeaumount, Veronica Gibaja, Kavitha Venkatesan, Robert Schlegel, William R. Sellers, Nicholas Keen, Jun Liu, Giordano Caponigro, Jordi Barretina, Vesselina G. Cooke, Charles Mullighan, Steven A. Carr, James R. Downing, Levi A. Garraway, Frank Stegmeier. Global chromatin profiling reveals NSD2 mutation in pediatric ALL. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2930. doi:10.1158/1538-7445.AM2014-2930
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Affiliation(s)
- Ho Man Chan
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | | | - Yan Wang
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | | | | | | | | | | | - Min Hu
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | - Nathan P. Englund
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | - Feng Yan
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
| | - Zhaofu Wang
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | | | - Lei Wei
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - Jing Ma
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - John Easton
- 4St. Jude Children's Research Hospital, Memphis, TN
| | - Zhengtian Yu
- 5Novartis Insts. for BioMedical Research, Shanghai, China
| | | | | | | | | | | | - Nicholas Keen
- 1Novartis Insts. for BioMedical Research, Cambridge, MA
| | - Jun Liu
- 3Genomic Institute of the Novartis Research Foundation, San Diego, CA
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Van Allen EM, Mouw KW, Kim P, Iyer G, Wagle N, Al-Ahmadie H, Zhu C, Ostrovnaya I, Kryukov GV, O'Connor KW, Sfakianos J, Garcia-Grossman I, Kim J, Guancial EA, Bambury R, Bahl S, Gupta N, Farlow D, Qu A, Signoretti S, Barletta JA, Reuter V, Boehm J, Lawrence M, Getz G, Kantoff P, Bochner BH, Choueiri TK, Bajorin DF, Solit DB, Gabriel S, D'Andrea A, Garraway LA, Rosenberg JE. Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma. Cancer Discov 2014; 4:1140-53. [PMID: 25096233 DOI: 10.1158/2159-8290.cd-14-0623] [Citation(s) in RCA: 441] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
UNLABELLED Cisplatin-based chemotherapy is the standard of care for patients with muscle-invasive urothelial carcinoma. Pathologic downstaging to pT0/pTis after neoadjuvant cisplatin-based chemotherapy is associated with improved survival, although molecular determinants of cisplatin response are incompletely understood. We performed whole-exome sequencing on pretreatment tumor and germline DNA from 50 patients with muscle-invasive urothelial carcinoma who received neoadjuvant cisplatin-based chemotherapy followed by cystectomy (25 pT0/pTis "responders," 25 pT2+ "nonresponders") to identify somatic mutations that occurred preferentially in responders. ERCC2, a nucleotide excision repair gene, was the only significantly mutated gene enriched in the cisplatin responders compared with nonresponders (q < 0.01). Expression of representative ERCC2 mutants in an ERCC2-deficient cell line failed to rescue cisplatin and UV sensitivity compared with wild-type ERCC2. The lack of normal ERCC2 function may contribute to cisplatin sensitivity in urothelial cancer, and somatic ERCC2 mutation status may inform cisplatin-containing regimen usage in muscle-invasive urothelial carcinoma. SIGNIFICANCE Somatic ERCC2 mutations correlate with complete response to cisplatin-based chemosensitivity in muscle-invasive urothelial carcinoma, and clinically identified mutations lead to cisplatin sensitivity in vitro. Nucleotide excision repair pathway defects may drive exceptional response to conventional chemotherapy.
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Affiliation(s)
- Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Harvard Radiation Oncology Program, Boston, Massachusetts
| | - Philip Kim
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Hikmat Al-Ahmadie
- Weill Cornell Medical College, Cornell University, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cong Zhu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Kevin W O'Connor
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - John Sfakianos
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ilana Garcia-Grossman
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Elizabeth A Guancial
- Division of Hematology/Oncology, Department of Medicine, University of Rochester Medical Center School of Medicine and Dentistry, Rochester, New York
| | - Richard Bambury
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samira Bahl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Deborah Farlow
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Angela Qu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Justine A Barletta
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Victor Reuter
- Weill Cornell Medical College, Cornell University, New York, New York. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesse Boehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, Massachusetts
| | - Philip Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Bernard H Bochner
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. Weill Cornell Medical College, Cornell University, New York, New York
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Dean F Bajorin
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stacey Gabriel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Harvard Radiation Oncology Program, Boston, Massachusetts
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
| | - Jonathan E Rosenberg
- Weill Cornell Medical College, Cornell University, New York, New York. Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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Helming KC, Wang X, Wilson BG, Vazquez F, Haswell JR, Manchester HE, Kim Y, Kryukov GV, Ghandi M, Aguirre AJ, Jagani Z, Wang Z, Garraway LA, Hahn WC, Roberts CWM. ARID1B is a specific vulnerability in ARID1A-mutant cancers. Nat Med 2014; 20:251-4. [PMID: 24562383 PMCID: PMC3954704 DOI: 10.1038/nm.3480] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/17/2014] [Indexed: 12/17/2022]
Abstract
Recent studies have revealed that ARID1A is frequently mutated across a wide variety of human cancers and also has bona fide tumor suppressor properties. Consequently, identification of vulnerabilities conferred by ARID1A mutation would have major relevance for human cancer. Here, using a broad screening approach, we identify ARID1B, a related but mutually exclusive homolog of ARID1A in the SWI/SNF chromatin remodeling complex, as the number one gene preferentially required for the survival of ARID1A-mutant cancer cell lines. We show that loss of ARID1B in ARID1A-deficient backgrounds destabilizes SWI/SNF and impairs proliferation. Intriguingly, we also find that ARID1A and ARID1B are frequently co-mutated in cancer, but that ARID1A-deficient cancers retain at least one ARID1B allele. These results suggest that loss of ARID1A and ARID1B alleles cooperatively promotes cancer formation but also results in a unique functional dependence. The results further identify ARID1B as a potential therapeutic target for ARID1A-mutant cancers.
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Affiliation(s)
- Katherine C Helming
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA. [4] Biological and Biomedical Sciences Program, Harvard Medical School, Boston, Massachusetts, USA. [5]
| | - Xiaofeng Wang
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA. [4]
| | - Boris G Wilson
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Francisca Vazquez
- 1] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jeffrey R Haswell
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Haley E Manchester
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Youngha Kim
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Boston, Massachusetts, USA
| | - Andrew J Aguirre
- 1] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Zainab Jagani
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - Zhong Wang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Levi A Garraway
- 1] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - William C Hahn
- 1] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [3] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Charles W M Roberts
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA. [4] Broad Institute of Harvard and MIT, Boston, Massachusetts, USA. [5] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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19
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Van Allen EM, Wagle N, Sucker A, Treacy DJ, Johannessen CM, Goetz EM, Place CS, Taylor-Weiner A, Whittaker S, Kryukov GV, Hodis E, Rosenberg M, McKenna A, Cibulskis K, Farlow D, Zimmer L, Hillen U, Gutzmer R, Goldinger SM, Ugurel S, Gogas HJ, Egberts F, Berking C, Trefzer U, Loquai C, Weide B, Hassel JC, Gabriel SB, Carter SL, Getz G, Garraway LA, Schadendorf D. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov 2013; 4:94-109. [PMID: 24265153 DOI: 10.1158/2159-8290.cd-13-0617] [Citation(s) in RCA: 683] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Most patients with BRAF(V600)-mutant metastatic melanoma develop resistance to selective RAF kinase inhibitors. The spectrum of clinical genetic resistance mechanisms to RAF inhibitors and options for salvage therapy are incompletely understood. We performed whole-exome sequencing on formalin-fixed, paraffin-embedded tumors from 45 patients with BRAF(V600)-mutant metastatic melanoma who received vemurafenib or dabrafenib monotherapy. Genetic alterations in known or putative RAF inhibitor resistance genes were observed in 23 of 45 patients (51%). Besides previously characterized alterations, we discovered a "long tail" of new mitogen-activated protein kinase (MAPK) pathway alterations (MAP2K2, MITF) that confer RAF inhibitor resistance. In three cases, multiple resistance gene alterations were observed within the same tumor biopsy. Overall, RAF inhibitor therapy leads to diverse clinical genetic resistance mechanisms, mostly involving MAPK pathway reactivation. Novel therapeutic combinations may be needed to achieve durable clinical control of BRAF(V600)-mutant melanoma. Integrating clinical genomics with preclinical screens may model subsequent resistance studies.
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Affiliation(s)
- Eliezer M Van Allen
- 1Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School; 2Department of Pathology, Massachusetts General Hospital Cancer Center, Boston; 3Broad Institute of MIT and Harvard; 4Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts; 5Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, Essen; 6German Cancer Consortium (DKTK); 7Department of Dermatology, Heidelberg University Hospital, Heidelberg; 8Department of Dermatology and Allergy, Hannover Medical School, Hannover; 9Department of Dermatology, University of Wuerzburg, Wuerzburg; 10Department of Dermatology, Venerology and Allergology, University of Schleswig-Holstein Hospital, Kiel; 11Department of Dermatology and Allergology, Ludwig-Maximilian University, Munich; 12Department of Dermatology, Venerology and Allergy, Charité Universitätsmedizin Berlin, Humboldt University, Berlin; 13Department of Dermatology, University of Mainz, Mainz; 14University Medical Center, University of Tübingen, Tübingen, Germany; 15Department of Genome Sciences, University of Washington, Seattle, Washington; 16Department of Dermatology, University Hospital Zurich, Zurich, Switzerland; and 17First Department of Medicine, Medical School, University of Athens, Athens, Greece
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20
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Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, Hon CSY, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, Schreiber SL. An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell 2013; 154:1151-1161. [PMID: 23993102 DOI: 10.1016/j.cell.2013.08.003] [Citation(s) in RCA: 495] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 06/21/2013] [Accepted: 08/01/2013] [Indexed: 01/18/2023]
Abstract
The high rate of clinical response to protein-kinase-targeting drugs matched to cancer patients with specific genomic alterations has prompted efforts to use cancer cell line (CCL) profiling to identify additional biomarkers of small-molecule sensitivities. We have quantitatively measured the sensitivity of 242 genomically characterized CCLs to an Informer Set of 354 small molecules that target many nodes in cell circuitry, uncovering protein dependencies that: (1) associate with specific cancer-genomic alterations and (2) can be targeted by small molecules. We have created the Cancer Therapeutics Response Portal (http://www.broadinstitute.org/ctrp) to enable users to correlate genetic features to sensitivity in individual lineages and control for confounding factors of CCL profiling. We report a candidate dependency, associating activating mutations in the oncogene β-catenin with sensitivity to the Bcl-2 family antagonist, navitoclax. The resource can be used to develop novel therapeutic hypotheses and to accelerate discovery of drugs matched to patients by their cancer genotype and lineage.
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Affiliation(s)
- Amrita Basu
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Jaime H Cheah
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Edmund V Price
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ke Liu
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | | | | | - Daisuke Ito
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephanie Wang
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Abigail L Bracha
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Mathias Wawer
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua C Gilbert
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew J Wilson
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Vlado Dancik
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - C Suk-Yee Hon
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Benito Munoz
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua A Bittker
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Dineo Khabele
- Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew M Stern
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Paul A Clemons
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Alykhan F Shamji
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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21
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Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013. [PMID: 23770567 DOI: 10.1038/nature12213.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
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Affiliation(s)
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Paz Polak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Gregory V Kryukov
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | | | | | - Scott L Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Craig H Mermel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Steven A Roberts
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Adam Kiezun
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Peter S Hammerman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Genome Sciences, University of Washington, Seattle, WA 98195
| | - Yotam Drier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.,Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lihua Zou
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Alex H Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Trevor J Pugh
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Elena Helman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lauren Ambrogio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | | | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Maria L Cortés
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Douglas Voet
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Daniel DiCara
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Pei Lin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Lee Lichtenstein
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - David I Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Timothy Fennell
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Marcin Imielinski
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Bryan Hernandez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Eran Hodis
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan Baca
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Austin M Dulak
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jens Lohr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dan-Avi Landau
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Yale Cancer Center, Department of Hematology, New Haven, CT
| | - Catherine J Wu
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | | | | | - Amnon Koren
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Steven A McCarroll
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Jaume Mora
- Department of Pediatric Oncology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Brian Crompton
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Robert Onofrio
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Wendy Winckler
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - Charles W M Roberts
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | | | - Kimberly Stegmaier
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Boston Children's Hospital, Boston, MA, 02115, USA
| | - Adam J Bass
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Levi A Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Dmitry A Gordenin
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
| | - Shamil Sunyaev
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Harvard Medical School, Boston, MA, 02115, USA.,Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA.,Massachusetts General Hospital, Boston, MA, 02114, USA
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22
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Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Punctuated evolution of prostate cancer genomes. Cell 2013; 153:666-77. [PMID: 23622249 DOI: 10.1016/j.cell.2013.03.021] [Citation(s) in RCA: 899] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/17/2013] [Accepted: 03/19/2013] [Indexed: 10/26/2022]
Abstract
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and progression. By modeling the genesis of genomic rearrangements, we identified abundant DNA translocations and deletions that arise in a highly interdependent manner. This phenomenon, which we term "chromoplexy," frequently accounts for the dysregulation of prostate cancer genes and appears to disrupt multiple cancer genes coordinately. Our modeling suggests that chromoplexy may induce considerable genomic derangement over relatively few events in prostate cancer and other neoplasms, supporting a model of punctuated cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we charted a path of oncogenic events along which chromoplexy may drive prostate carcinogenesis.
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23
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Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Van Allen E, Kryukov GV, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Voet D, Saksena G, Cipicchio MR, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Abstract 4601: Punctuated evolution of prostate cancer genomes. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of alterations across the entire genome has not been profiled extensively in this disease. We sequenced the genomes of 55 primary prostate tumors and matched normal tissues to catalogue somatic alterations and to study how they accumulate during oncogenesis and progression. By implementing an algorithm to identify genomic alterations that arise together, we found abundant sets of DNA rearrangements and deletions that may occur simultaneously in a single cell. This phenomenon, which we term “chromoplexy," frequently accounts for the dysregulation of prostate cancer genes including PTEN, NKX3-1, TP53 and CDKN1B. The somatic fusion of TMPRSS2 and ERG, which occurs in approximately half of prostate cancers, predominantly arises with additional genomic rearrangements in the context of chromoplexy. We further demonstrate that TMPRSS2-ERG fusion-positive tumors display a unique profile of chromoplexy, with complex chains of rearrangements that may fuse DNA from four or more distinct chromosomes.
In prostate cancer and other neoplasms, chromoplexy induces considerable genomic derangement in a series of relatively few events. In several instances, multiple cancer genes from non-contiguous regions of the genome appear to be disrupted simultaneously by this process, suggesting a model of punctuated progression during cancer evolution. By characterizing the clonal hierarchy of genomic lesions in prostate tumors, we constructed a path of oncogenic events along which chromoplexy drives prostate carcinogenesis.
Citation Format: Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Eliezer Van Allen, Gregory V. Kryukov, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Douglas Voet, Gordon Saksena, Michelle R. Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway. Punctuated evolution of prostate cancer genomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4601. doi:10.1158/1538-7445.AM2013-4601
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Affiliation(s)
| | | | | | | | | | - Yotam Drier
- 5Weizmann Institute of Science, Rehovot, Israel
| | - Kyung Park
- 4Weill Cornell Medical College, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gad Getz
- 3The Broad Institute, Cambridge, MA
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24
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Prandi D, Baca SC, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Van Allen E, Kryukov GV, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Abstract 4017: Dissecting the clonal hierarchy of cancer-driving genomic lesions. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-4017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Characterizing the genomic evolution of cancer is critical to understanding disease progression and identifying potential therapeutic targets. By examining the clonal hierarchy of genomic lesions in common tumors, it would be possible to reconstruct the path of oncogenic events that drive carcinogenesis. Reliable assessment of such paths from high-throughput genome sequencing data is complicated by the admixture of normal DNA in tumor samples and by reduced data signal for highly subclonal events. We introduce an approach that exploits individuals’ genetic background by using the abundant germline SNP genotype data provided by whole genome sequence coverage to assess the clonality of genomic alterations, including copy number changes, rearrangements, and point mutations.
We developed a novel algorithm, CLONET (CLONality Estimate in Tumors), which analyzes patient-specific heterozygous SNP loci (informative SNPs) and mono-allelic somatic deletions to assess levels of stromal DNA admixture and infer the clonal status of each aberration. For every mono allelic deletion, CLONET assesses the allelic fractions of informative SNPs to determine the apparent proportion of normal cells DNA. Next, through a conservative use of simulation-based error estimates, deletions with the lowest proportions of normal DNA reads are considered clonal. For point mutations, the tumor allelic fraction is corrected for stromal DNA admixture level and subclonality is inferred when it differs significantly from the expected value for clonal lesions. Similarly, the proportions of reads that span each side of a putative breakpoint involved in a rearrangement are matched against the expected values. CLONET also addresses tumor aneuploidy by searching for chromosomes with coverage and allelic fractions of informative SNPs not consistent with a diploid genome.
CLONET was tested on 55 whole genome sequences from prostate cancers, a highly heterogeneous tumor type, to catalogue the accumulation of somatic alterations during oncogenesis and progression. In 98% of the cases CLONET made confident assessment of admixture and clonality. We observed consistent clonal lesions involving NKX3-1, the 3Mb region between TMPRSS2 and ERG and FOXP1, as well as early point mutations in SPOP and FOXA1. Overall, we observed a higher rate of subclonal protein-coding point mutation versus deletions (p-value < 10−7). We validated this approach by IHC and FISH for predicted clonal and sub-clonal events. A predicted subclonal homozygous deletion of CHD1 was confirmed by FISH that demonstrated the presence of both nuclei with homozygous and with hemizygous deletion of CHD1. Finally, to assess the general validity of CLONET, we analyzed data from 53 additional tumor genomes, including 25 melanomas and 28 lung adenocarcinomas.
In summary, our results imply the existence of consensus paths of tumor carcinogenesis that favor dysregulation of cancer genes in a defined sequence.
Citation Format: Davide Prandi, Sylvan C. Baca, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Eliezer Van Allen, Gregory V. Kryukov, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway. Dissecting the clonal hierarchy of cancer-driving genomic lesions. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4017. doi:10.1158/1538-7445.AM2013-4017
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Affiliation(s)
| | | | | | - Juan Miguel Mosquera
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | | | - Yotam Drier
- 3The Broad Institute of Harvard and MIT, Cambridge, MA
| | - Kyung Park
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Naoki Kitabayashi
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Theresa Y. MacDonald
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | | | | | | | - T. David Soong
- 5Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | | | | | - Ashutosh Tewari
- 6LeFrak Institute of Robotic Surgery and Prostate Cancer Institute, James Buchanan Brady Foundation Department of Urology, Weill Medical College of Cornell University, New York, NY
| | - Himisha Beltran
- 7Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medical College, New York, NY
| | | | - Gunther Boysen
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | | | - Christopher E. Barbieri
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | | | | | | | | | - Douglas Voet
- 3The Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | | | | | - Michael F. Berger
- 8Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Todd R. Golub
- 3The Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | - Olivier Elemento
- 5Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Gad Getz
- 3The Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - Mark A. Rubin
- 4Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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25
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Abstract
Systematic sequencing of human cancer genomes has identified many recurrent mutations in the protein-coding regions of genes but rarely in gene regulatory regions. Here, we describe two independent mutations within the core promoter of telomerase reverse transcriptase (TERT), the gene coding for the catalytic subunit of telomerase, which collectively occur in 50 of 70 (71%) melanomas examined. These mutations generate de novo consensus binding motifs for E-twenty-six (ETS) transcription factors, and in reporter assays, the mutations increased transcriptional activity from the TERT promoter by two- to fourfold. Examination of 150 cancer cell lines derived from diverse tumor types revealed the same mutations in 24 cases (16%), with preliminary evidence of elevated frequency in bladder and hepatocellular cancer cells. Thus, somatic mutations in regulatory regions of the genome may represent an important tumorigenic mechanism.
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Affiliation(s)
- Franklin W. Huang
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
| | - Eran Hodis
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Harvard Medical School, Boston, MA 02115
- Harvard–MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mary Jue Xu
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Harvard Medical School, Boston, MA 02115
- Harvard–MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Lynda Chin
- Department of Genomic Medicine, M.D. Anderson Cancer Center, Houston, TX 77030
- Institute for Applied Cancer Science, M.D. Anderson Cancer Center, Houston, TX 77030
| | - Levi A. Garraway
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Medical School, Boston, MA 02115
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26
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, J.Wilson C, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. [DOI: 10.1038/nature11735] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DSB, Schadendorf D, Lander ES, Gabriel SB, Getz G, Garraway LA, Chin L. A landscape of driver mutations in melanoma. Cell 2012; 150:251-63. [PMID: 22817889 DOI: 10.1016/j.cell.2012.06.024] [Citation(s) in RCA: 1890] [Impact Index Per Article: 157.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 06/12/2012] [Accepted: 06/25/2012] [Indexed: 12/30/2022]
Abstract
Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic UV light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19, and ARID2), three of which-RAC1, PPP6C, and STK19-harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis.
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Affiliation(s)
- Eran Hodis
- The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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28
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Roberts SA, Sterling J, Thompson C, Harris S, Mav D, Shah R, Klimczak LJ, Kryukov GV, Malc E, Mieczkowski PA, Resnick MA, Gordenin DA. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol Cell 2012; 46:424-35. [PMID: 22607975 DOI: 10.1016/j.molcel.2012.03.030] [Citation(s) in RCA: 323] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 03/14/2012] [Accepted: 03/31/2012] [Indexed: 10/28/2022]
Abstract
Mutations are typically perceived as random, independent events. We describe here nonrandom clustered mutations in yeast and in human cancers. Genome sequencing of yeast grown under chronic alkylation damage identified mutation clusters that extend up to 200 kb. A predominance of "strand-coordinated" changes of either cytosines or guanines in the same strand, mutation patterns, and genetic controls indicated that simultaneous mutations were generated by base alkylation in abnormally long single-strand DNA (ssDNA) formed at double-strand breaks (DSBs) and replication forks. Significantly, we found mutation clusters with analogous features in sequenced human cancers. Strand-coordinated clusters of mutated cytosines or guanines often resided near chromosome rearrangement breakpoints and were highly enriched with a motif targeted by APOBEC family cytosine-deaminases, which strongly prefer ssDNA. These data indicate that hypermutation via multiple simultaneous changes in randomly formed ssDNA is a general phenomenon that may be an important mechanism producing rapid genetic variation.
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Affiliation(s)
- Steven A Roberts
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, NC 27709, USA
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29
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Stransky N, Kryukov GV, Caponigro G, Barretina J, Venkatesan K, Margolin AA, Wilson CJ, Lehar J, Jones MD, Palescandolo E, Sougnez C, Onofrio RC, MacConaill L, Ardlie K, Golub TR, Morrissey M, Selers WR, Schlegel R, Garraway LA. Abstract 5114: Integrative analysis of the Cancer Cell Line Encyclopedia reveals genetic and transcriptional predictors of compound sensitivity. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Cancer Cell Line Encyclopedia (CCLE) represents a collaborative effort to assemble a comprehensive resource of human cancer models for basic and translational research. It contains a detailed genetic profiling of approximately 1,000 human cancer cell lines spanning many tumor types. Thus far, high-density SNP array data, gene expression microarray data and mutation data from hybrid capture sequencing of 1,650 cancer genes has been obtained. Additionally, we have assessed the sensitivity of these same cell lines using a series of pharmacological compounds that represent both conventional cytotoxic and targeted agents. On major goal of the CCLE effort involves systematic integration of the genomic and pharmacologic datasets in order to identify putative targets of prevalent genetic alterations as well as predictors and modifiers of pharmacologic sensitivity and resistance. The availability of high-quality data generated by uniform criteria across hundreds of cell lines markedly enhances the statistical power to discover genetic alterations involved in carcinogenesis and molecular predictors of pharmacologic vulnerability. We developed a framework based on an elastic net machine-learning regression algorithm, and combined with a bootstrapping procedure, to derive predictive models of the sensitivity to each compound, using all genetic features of the cell lines in the collection. Through this computational prediction approach, we have both rediscovered molecular features predicting response to most drugs in our set but also uncovered novel potential biomarkers of sensitivity and resistance to targeted agents and chemotherapy drugs. For instance, we have found that response to topoisomerase 1 inhibitors seems to be linked to the expression of a single gene. We have also observed that tissue lineage is a key predictor for sensitivity to certain compounds, providing rationale for clinical trials of these drugs in particular cancer types and we identified potential stratifiers for existing EGFR targeted therapies. Finally, we have found an additional target for a certain chemotype of MEK inhibitors, and shown that this interaction was responsible for growth suppression, which might be a new indication for this kind of drug. Our cell line-based platform provides a valuable tool for the development of personalized cancer medicine, revealing critical tumor dependencies and helping to stratify patients for clinical trials.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5114. doi:1538-7445.AM2012-5114
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30
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483:603-7. [PMID: 22460905 PMCID: PMC3320027 DOI: 10.1038/nature11003] [Citation(s) in RCA: 5289] [Impact Index Per Article: 440.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 03/01/2012] [Indexed: 02/07/2023]
Abstract
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Cell Lineage
- Chromosomes, Human/genetics
- Clinical Trials as Topic/methods
- Databases, Factual
- Drug Screening Assays, Antitumor/methods
- Encyclopedias as Topic
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, ras/genetics
- Genome, Human/genetics
- Genomics
- Humans
- Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors
- Mitogen-Activated Protein Kinase Kinases/metabolism
- Models, Biological
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Pharmacogenetics
- Plasma Cells/cytology
- Plasma Cells/drug effects
- Plasma Cells/metabolism
- Precision Medicine/methods
- Receptor, IGF Type 1/antagonists & inhibitors
- Receptor, IGF Type 1/metabolism
- Receptors, Aryl Hydrocarbon/genetics
- Receptors, Aryl Hydrocarbon/metabolism
- Sequence Analysis, DNA
- Topoisomerase Inhibitors/pharmacology
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Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Adam A. Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | | | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Gregory V. Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael F. Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - John E. Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Felipa A. Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Ingo H. Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Guoying K. Yu
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Michael D. Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Robert C. Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Jill P. Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Stacey B. Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Vic E. Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Barbara L. Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jennifer L. Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Todd R. Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Michael P. Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - William R. Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Levi A. Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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31
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. [PMID: 22460905 DOI: 10.1038/nature1100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
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Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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32
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Lachke SA, Ho JWK, Kryukov GV, O'Connell DJ, Aboukhalil A, Bulyk ML, Park PJ, Maas RL. iSyTE: integrated Systems Tool for Eye gene discovery. Invest Ophthalmol Vis Sci 2012; 53:1617-27. [PMID: 22323457 DOI: 10.1167/iovs.11-8839] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE To facilitate the identification of genes associated with cataract and other ocular defects, the authors developed and validated a computational tool termed iSyTE (integrated Systems Tool for Eye gene discovery; http://bioinformatics.udel.edu/Research/iSyTE). iSyTE uses a mouse embryonic lens gene expression data set as a bioinformatics filter to select candidate genes from human or mouse genomic regions implicated in disease and to prioritize them for further mutational and functional analyses. METHODS Microarray gene expression profiles were obtained for microdissected embryonic mouse lens at three key developmental time points in the transition from the embryonic day (E)10.5 stage of lens placode invagination to E12.5 lens primary fiber cell differentiation. Differentially regulated genes were identified by in silico comparison of lens gene expression profiles with those of whole embryo body (WB) lacking ocular tissue. RESULTS Gene set analysis demonstrated that this strategy effectively removes highly expressed but nonspecific housekeeping genes from lens tissue expression profiles, allowing identification of less highly expressed lens disease-associated genes. Among 24 previously mapped human genomic intervals containing genes associated with isolated congenital cataract, the mutant gene is ranked within the top two iSyTE-selected candidates in approximately 88% of cases. Finally, in situ hybridization confirmed lens expression of several novel iSyTE-identified genes. CONCLUSIONS iSyTE is a publicly available Web resource that can be used to prioritize candidate genes within mapped genomic intervals associated with congenital cataract for further investigation. Extension of this approach to other ocular tissue components will facilitate eye disease gene discovery.
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Affiliation(s)
- Salil A Lachke
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard edical School, Boston, Massachusetts, USA
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33
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Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature 2011; 479:223-7. [PMID: 21993625 PMCID: PMC3319411 DOI: 10.1038/nature10533] [Citation(s) in RCA: 412] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 09/05/2011] [Indexed: 11/15/2022]
Abstract
The naked mole rat (NMR, Heterocephalus glaber) is a strictly subterranean, extraordinarily long-lived eusocial mammal1. Although the size of a mouse, its maximum lifespan exceeds 30 years and makes this animal the longest living rodent. NMRs show negligible senescence, no age-related increase in mortality, and high fecundity until death2. In addition to delayed aging, NMRs are resistant to both spontaneous cancer and experimentally induced tumorigenesis3,4. NMRs pose a challenge to the theories that link aging, cancer and redox homeostasis. Although characterized by significant oxidative stress5, the NMR proteome does not show age-related susceptibility to oxidative damage nor increased ubiquitination6. NMRs naturally reside in large colonies with a single breeding female, the “queen,” who suppresses the sexual maturity of her subordinates11. NMRs also live in full darkness, at low oxygen and high carbon dioxide concentrations7, and are unable to sustain thermogenesis8 nor feel certain types of pain9,10. Here we report sequencing and analysis of the NMR genome, which revealed unique genome features and molecular adaptations consistent with cancer resistance, poikilothermy, hairlessness, altered visual function, circadian rhythms and taste sensing, and insensitivity to low oxygen. This information provides insights into NMR’s exceptional longevity and capabilities to live in hostile conditions, in the dark and at low oxygen. The extreme traits of NMR, together with the reported genome and transcriptome information, offer unprecedented opportunities for understanding aging and advancing many other areas of biological and biomedical research.
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Affiliation(s)
- Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul, 120-750, Korea
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Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence M, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortés ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio R, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR. The mutational landscape of head and neck squamous cell carcinoma. Science 2011; 333:1157-60. [PMID: 21798893 PMCID: PMC3415217 DOI: 10.1126/science.1208130] [Citation(s) in RCA: 1886] [Impact Index Per Article: 145.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.
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Affiliation(s)
- Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ann Marie Egloff
- Department of Otolaryngology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Aaron D. Tward
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Otology and Laryngology, Harvard Medical School, Boston, MA 02114, USA
- Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | | | | | | | - Gregory V. Kryukov
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron McKenna
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Erica Shefler
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex H. Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott L. Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Douglas Voet
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maria L Cortés
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Gordon Saksena
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Candace Guiducci
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Onofrio
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marjorie Romkes
- Department of Medicine, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15261, USA
| | - Joel L. Weissfeld
- Department of Epidemiology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
| | - Raja R. Seethala
- Department of Pathology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Lin Wang
- Department of Pathology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | | | | | | | | | - Wendy Winckler
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Eric S. Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Todd R. Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Levi A. Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jennifer R. Grandis
- Department of Otolaryngology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
- Department of Pharmacology, University of Pittsburgh and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
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Kryukov GV, Berger MF, Stransky N, Barretina J, Onofrio R, Caponigro G, Sougnez C, Monahan J, Shefler E, Venkhatesan K, Cibulskis K, Morais P, Sivachenko A, Meltzer J, Lawrence M, Ramos A, Getz G, Platform BGS, Thibault J, Mahan S, Jones M, Morrissey M, Sonkin D, Ardlie KG, Golub T, Weber B, Warmuth M, Sellers W, Harris J, Schlegel R, Garraway LA. Abstract 923: Separating the wheat from the chaff: A first look at the Cancer Cell Lines Encyclopedia sequencing data. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Comprehensive characterization of cancer genomic alterations and understanding their functional roles are important steps in the development of personalized cancer treatments. The Cancer Cell Lines Encyclopedia project aims to relate genomic alterations to drug sensitivity of cancer cells. Cancer cell lines are indispensable resource for researchers because of their convenience for high-throughput profiling and availability for follow-up experiments.
We sequenced the coding regions of 1645 genes in over 800 cancer cell lines representing 32 different tumor types. Genes were selected on their likelihood to be cancer-related and sequenced using next-generation Illumina technology after hybrid selection of exonic regions. Although, the absence of matched normal cell lines precludes direct distinction of somatic from germline mutations, we were able to select a subset of mutations highly enriched in somatic events combining the following three approaches: subtraction of known polymorphisms, prediction of strongly detrimental mutations (including computational predictions of amino acid substitutions’ effects on protein function) and detection of abnormal linkage disequilibrium patterns for recurring mutations.
We then searched for the three independent indicators of the potential involvement of mutated genes in cancer: the presence of an unusually high fraction of strongly damaging mutations within a gene, statistically significant deviation of distribution of mutations between cancer types from random expectation and clustering of mutations within a gene. Combined analysis of these lines of evidence revealed both known and novel potential tumor suppressors and oncogenes.
These data should become an import resource for cancer researchers in their search for personalized cancer therapies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 923. doi:10.1158/1538-7445.AM2011-923
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Affiliation(s)
| | | | | | | | | | | | | | - John Monahan
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Erica Shefler
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Paula Morais
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Jodi Meltzer
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Alex Ramos
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Gad Getz
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Joseph Thibault
- 3Genomics Institute of the Novartis Research Foundation, San Diego, CA
| | - Scott Mahan
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael Jones
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Dmitry Sonkin
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Todd Golub
- 1The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Barbara Weber
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Markus Warmuth
- 2Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Jennifer Harris
- 3Genomics Institute of the Novartis Research Foundation, San Diego, CA
| | | | - Levi A. Garraway
- 4Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
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Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 2010; 86:832-8. [PMID: 20471002 DOI: 10.1016/j.ajhg.2010.04.005] [Citation(s) in RCA: 587] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 03/29/2010] [Accepted: 04/15/2010] [Indexed: 01/24/2023] Open
Abstract
Deep sequencing will soon generate comprehensive sequence information in large disease samples. Although the power to detect association with an individual rare variant is limited, pooling variants by gene or pathway into a composite test provides an alternative strategy for identifying susceptibility genes. We describe a statistical method for detecting association of multiple rare variants in protein-coding genes with a quantitative or dichotomous trait. The approach is based on the regression of phenotypic values on individuals' genotype scores subject to a variable allele-frequency threshold, incorporating computational predictions of the functional effects of missense variants. Statistical significance is assessed by permutation testing with variable thresholds. We used a rigorous population-genetics simulation framework to evaluate the power of the method, and we applied the method to empirical sequencing data from three disease studies.
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Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res 2009; 19:1606-15. [PMID: 19525355 DOI: 10.1101/gr.092213.109] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads derived from a single Illumina Genome Analyzer lane, approximately 94% (approximately 50,500) target sites can be observed with at least one read. The uniformity of coverage was also greatly improved; up to 93% and 57% of all targets fell within a 100- and 10-fold coverage range, respectively. Alleles at >400,000 target base positions were determined across six subjects and examined for single nucleotide polymorphisms (SNPs), and the concordance with independently obtained genotypes was 98.4%-100%. We detected >500 SNPs not currently in dbSNP, 362 of which were in targeted CpG locations. Transitions in CpG sites were at least 13.7 times more abundant than non-CpG transitions. Fractions of polymorphic CpG sites are lower in CpG-rich regions and show higher correlation with human-chimpanzee divergence within CpG versus non-CpG sites. This is consistent with the hypothesis that methylation rate heterogeneity along chromosomes contributes to mutation rate variation in humans. Our success suggests that targeted CpG resequencing is an efficient way to identify common and rare genetic variations. In addition, the significantly improved padlock capture technology can be readily applied to other projects that require multiplex sample preparation.
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Affiliation(s)
- Jin Billy Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
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38
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Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nat Genet 2009; 41:393-5. [PMID: 19287383 DOI: 10.1038/ng.363] [Citation(s) in RCA: 293] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 02/24/2009] [Indexed: 11/09/2022]
Abstract
Eukaryotic DNA replication is highly stratified, with different genomic regions shown to replicate at characteristic times during S phase. Here we observe that mutation rate, as reflected in recent evolutionary divergence and human nucleotide diversity, is markedly increased in later-replicating regions of the human genome. All classes of substitutions are affected, suggesting a generalized mechanism involving replication time-dependent DNA damage. This correlation between mutation rate and regionally stratified replication timing may have substantial evolutionary implications.
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39
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Xu XM, Carlson BA, Zhang Y, Mix H, Kryukov GV, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea. Biol Trace Elem Res 2007; 119:234-41. [PMID: 17916946 DOI: 10.1007/s12011-007-8003-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 12/14/2022]
Abstract
We used comparative genomics and experimental analyses to show that (1) eukaryotes and archaea, which possess the selenocysteine (Sec) protein insertion machinery contain an enzyme, O-phosphoseryl-transfer RNA (tRNA) [Ser]Sec kinase (designated PSTK), which phosphorylates seryl-tRNA [Ser]Sec to form O-phosphoseryl-tRNA [Ser]Sec and (2) the Sec synthase (SecS) in mammals is a pyridoxal phosphate-containing protein previously described as the soluble liver antigen (SLA). SecS uses the product of PSTK, O-phosphoseryl-tRNA[Ser]Sec, and selenophosphate as substrates to generate selenocysteyl-tRNA [Ser]Sec. Sec could be synthesized on tRNA [Ser]Sec from selenide, adenosine triphosphate (ATP), and serine using tRNA[Ser]Sec, seryl-tRNA synthetase, PSTK, selenophosphate synthetase, and SecS. The enzyme that synthesizes monoselenophosphate is a previously identified selenoprotein, selenophosphate synthetase 2 (SPS2), whereas the previously identified mammalian selenophosphate synthetase 1 did not serve this function. Monoselenophosphate also served directly in the reaction replacing ATP, selenide, and SPS2, demonstrating that this compound was the active selenium donor. Conservation of the overall pathway of Sec biosynthesis suggests that this pathway is also active in other eukaryotes and archaea that contain selenoproteins.
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Affiliation(s)
- Xue-Ming Xu
- Molecular Biology of Selenium Section, Laboratory of Cancer Prevention, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
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40
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Kryukov GV, Pennacchio LA, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet 2007; 80:727-39. [PMID: 17357078 PMCID: PMC1852724 DOI: 10.1086/513473] [Citation(s) in RCA: 444] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 01/30/2007] [Indexed: 12/31/2022] Open
Abstract
The accumulation of mildly deleterious missense mutations in individual human genomes has been proposed to be a genetic basis for complex diseases. The plausibility of this hypothesis depends on quantitative estimates of the prevalence of mildly deleterious de novo mutations and polymorphic variants in humans and on the intensity of selective pressure against them. We combined analysis of mutations causing human Mendelian diseases, of human-chimpanzee divergence, and of systematic data on human genetic variation and found that ~20% of new missense mutations in humans result in a loss of function, whereas ~27% are effectively neutral. Thus, the remaining 53% of new missense mutations have mildly deleterious effects. These mutations give rise to many low-frequency deleterious allelic variants in the human population, as is evident from a new data set of 37 genes sequenced in >1,500 individual human chromosomes. Surprisingly, up to 70% of low-frequency missense alleles are mildly deleterious and are associated with a heterozygous fitness loss in the range 0.001-0.003. Thus, the low allele frequency of an amino acid variant can, by itself, serve as a predictor of its functional significance. Several recent studies have reported a significant excess of rare missense variants in candidate genes or pathways in individuals with extreme values of quantitative phenotypes. These studies would be unlikely to yield results if most rare variants were neutral or if rare variants were not a significant contributor to the genetic component of phenotypic inheritance. Our results provide a justification for these types of candidate-gene (pathway) association studies and imply that mutation-selection balance may be a feasible evolutionary mechanism underlying some common diseases.
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Affiliation(s)
- Gregory V Kryukov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02125, USA
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41
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Novoselov SV, Kryukov GV, Xu XM, Carlson BA, Hatfield DL, Gladyshev VN. Selenoprotein H is a nucleolar thioredoxin-like protein with a unique expression pattern. J Biol Chem 2007; 282:11960-8. [PMID: 17337453 DOI: 10.1074/jbc.m701605200] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human selenoproteome consists of 25 known selenoproteins, but functions of many of these proteins are not known. Selenoprotein H (SelH) is a recently discovered 14-kDa mammalian protein with no sequence homology to functionally characterized proteins. By sensitive sequence and structure analyses, we identified SelH as a thioredoxin fold-like protein in which a conserved CXXU motif (cysteine separated by two other residues from selenocysteine) corresponds to the CXXC motif in thioredoxins. These data suggest a redox function of SelH. Indeed, a recombinant SelH shows significant glutathione peroxidase activity. In addition, SelH has a conserved RKRK motif in the N-terminal sequence. We cloned wild-type and cysteine mutant forms of SelH either upstream or downstream of green fluorescent protein (GFP) and localized this fusion protein to the nucleus in transfected mammalian cells, whereas mutations in the RKRK motif resulted in the cytosolic protein. Interestingly, the full-length SelH-GFP fusion protein localized specifically to nucleoli, whereas the N-terminal sequence of SelH fused to GFP had a diffuse nucleoplasm location. Northern blot analyses revealed low expression levels of SelH mRNA in various mouse tissues, but it was elevated in the early stages of embryonic development. In addition, SelH mRNA was overexpressed in human prostate cancer LNCaP and mouse lung cancer LCC1 cells. Down-regulation of SelH by RNA interference made LCC1 cells more sensitive to hydrogen peroxide but not to other peroxides tested. Overall, these data establish SelH as a novel nucleolar oxidoreductase and suggest that some functions in this compartment are regulated by redox and dependent on the trace element selenium.
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Affiliation(s)
- Sergey V Novoselov
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588, USA
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Lobanov AV, Kryukov GV, Hatfield DL, Gladyshev VN. Is there a twenty third amino acid in the genetic code? Trends Genet 2006; 22:357-60. [PMID: 16713651 DOI: 10.1016/j.tig.2006.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 03/17/2006] [Accepted: 05/05/2006] [Indexed: 11/20/2022]
Abstract
The universal genetic code includes 20 common amino acids. In addition, selenocysteine (Sec) and pyrrolysine (Pyl), known as the twenty first and twenty second amino acids, are encoded by UGA and UAG, respectively, which are the codons that usually function as stop signals. The discovery of Sec and Pyl suggested that the genetic code could be further expanded by reprogramming stop codons. To search for the putative twenty third amino acid, we employed various tRNA identification programs that scanned 16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals. Our data suggest that the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely.
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Affiliation(s)
- Alexey V Lobanov
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
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Abstract
Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifying selection. Furthermore, conservation of CNGs may be caused by mutation rate variation rather than selective constraints. To account for the effect of selective sampling, we have examined conservation of CNGs in taxa whose evolution is largely independent of the taxa from which the CNGs were initially identified, and we have controlled for mutation rate variation in the genome. We show that selective constraints in CNGs and their flanks are about one-half as strong in hominids as in murids, implying that hominids have accumulated many slightly deleterious mutations in functionally important nongenic regions. This is likely to be a consequence of the low effective population size of hominids leading to a reduced effectiveness of selection. We estimate that there are one and two times as many conserved nucleotides in CNGs as in known protein-coding genes of hominids and murids, respectively. Polymorphism frequencies in CNGs indicate that purifying selection operates in these sequences. During hominid evolution, we estimate that a total of about three deleterious mutations in CNGs and protein-coding genes have been selectively eliminated per diploid genome each generation, implying that deleterious mutations are eliminated from populations non-independently and that sex is necessary for long-term population persistence.
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Affiliation(s)
- Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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44
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Abstract
The use of selenocysteine (Sec) as the 21st amino acid in the genetic code has been described in all three major domains of life. However, within eukaryotes, selenoproteins are only known in animals and algae. In this study, we characterized selenoproteomes and Sec insertion systems in protozoan Apicomplexa parasites. We found that among these organisms, Plasmodium and Toxoplasma utilized Sec, whereas Cryptosporidium did not. However, Plasmodium had no homologs of known selenoproteins. By searching computationally for evolutionarily conserved selenocysteine insertion sequence (SECIS) elements, which are RNA structures involved in Sec insertion, we identified four unique Plasmodium falciparum selenoprotein genes. These selenoproteins were incorrectly annotated in PlasmoDB, were conserved in other Plasmodia and had no detectable homologs in other species. We provide evidence that two Plasmodium SECIS elements supported Sec insertion into parasite and endogenous selenoproteins when they were expressed in mammalian cells, demonstrating that the Plasmodium SECIS elements are functional and indicating conservation of Sec insertion between Apicomplexa and animals. Dependence of the plasmodial parasites on selenium suggests possible strategies for antimalarial drug development.
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Affiliation(s)
- Alexey V. Lobanov
- Department of Biochemistry, University of NebraskaLincoln, NE 68588, USA
| | - Cesar Delgado
- Department of Biochemistry, University of NebraskaLincoln, NE 68588, USA
- Department of Computer Science, University of NebraskaLincoln, NE 68588, USA
| | - Stefan Rahlfs
- Interdisziplinäres Forschungszentrum, Justus-Liebig University GiessenHeinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | | | - Gregory V. Kryukov
- Department of Biochemistry, University of NebraskaLincoln, NE 68588, USA
| | - Stephan Gromer
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 504D-69120 Heidelberg, Germany
| | - Dolph L. Hatfield
- Molecular Biology of Selenium Section, Laboratory of Cancer Prevention, National Cancer Institute, National Institutes of HealthBethesda, MD 20892, USA
| | - Katja Becker
- Interdisziplinäres Forschungszentrum, Justus-Liebig University GiessenHeinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Vadim N. Gladyshev
- Department of Biochemistry, University of NebraskaLincoln, NE 68588, USA
- To whom correspondence should be addressed. Tel: +1 402 472 4948; Fax: +1 402 472 7842;
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Abstract
Comparison of human and mouse genomes has revealed that many non-coding regions have levels of sequence conservation similar to protein-coding genes. These regions have attracted a lot of attention as potentially functional genomic sequences. However, little is known about the effect mutations in these conserved non-coding regions have on fitness and how many of them are present in the human genome as deleterious polymorphisms. To gain insight into the selective constraints imposed on conserved non-coding and protein-coding regions, we compared substitution rates in primate and rodent lineages and analyzed the density and allele frequencies of human polymorphism. Genomic regions conserved between primate and rodent groups show higher relative conservation within rodents than within primates. Thus, our analysis indicates a genome-wide relaxation of selective constraint in the primate lineage, which most likely resulted from a smaller effective population size. We found that this relaxation is much more profound in conserved non-coding regions than in protein-coding regions, and that mutations at a large proportion of sites in conserved non-coding regions are associated with very small fitness effect. Data on human polymorphism are also consistent with very weak selection in conserved non-coding regions. This staggering enrichment in sites at the borderline of neutrality can be explained by assuming an important role for synergistic epistasis in the evolution of non-coding regions. Our results suggest that most individual mutations in conserved non-coding regions are only slightly deleterious but are numerous and may have a significant cumulative impact on fitness.
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Affiliation(s)
- Gregory V Kryukov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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46
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Taskov K, Chapple C, Kryukov GV, Castellano S, Lobanov AV, Korotkov KV, Guigó R, Gladyshev VN. Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res 2005; 33:2227-38. [PMID: 15843685 PMCID: PMC1083425 DOI: 10.1093/nar/gki507] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly.
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Affiliation(s)
| | - Charles Chapple
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Centre de Regulació genòmicaDr Aiguader 80, 08003 Barcelona, Catalonia, Spain
| | | | - Sergi Castellano
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Centre de Regulació genòmicaDr Aiguader 80, 08003 Barcelona, Catalonia, Spain
| | | | | | - Roderic Guigó
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Centre de Regulació genòmicaDr Aiguader 80, 08003 Barcelona, Catalonia, Spain
| | - Vadim N. Gladyshev
- To whom correspondence should be addressed. Tel: +1 402 472 4948; Fax: +1 402 472 7842;
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47
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Castellano S, Novoselov SV, Kryukov GV, Lescure A, Blanco E, Krol A, Gladyshev VN, Guigó R. Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep 2004; 5:71-7. [PMID: 14710190 PMCID: PMC1298953 DOI: 10.1038/sj.embor.7400036] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2003] [Revised: 10/15/2003] [Accepted: 10/15/2003] [Indexed: 11/09/2022] Open
Abstract
While the genome sequence and gene content are available for an increasing number of organisms, eukaryotic selenoproteins remain poorly characterized. The dual role of the UGA codon confounds the identification of novel selenoprotein genes. Here, we describe a comparative genomics approach that relies on the genome-wide prediction of genes with in-frame TGA codons, and the subsequent comparison of predictions from different genomes, wherein conservation in regions flanking the TGA codon suggests selenocysteine coding function. Application of this method to human and fugu genomes identified a novel selenoprotein family, named SelU, in the puffer fish. The selenocysteine-containing form also occurred in other fish, chicken, sea urchin, green algae and diatoms. In contrast, mammals, worms and land plants contained cysteine homologues. We demonstrated selenium incorporation into chicken SelU and characterized the SelU expression pattern in zebrafish embryos. Our data indicate a scattered evolutionary distribution of selenoproteins in eukaryotes, and suggest that, contrary to the picture emerging from data available so far, other taxa-specific selenoproteins probably exist.
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Affiliation(s)
- Sergi Castellano
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Catalonia, Spain
| | - Sergey V Novoselov
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 65588, USA
| | - Gregory V Kryukov
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 65588, USA
| | - Alain Lescure
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - Enrique Blanco
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Catalonia, Spain
| | - Alain Krol
- UPR 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 Rue René Descartes, 67084 Strasbourg Cedex, France
| | - Vadim N Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 65588, USA
| | - Roderic Guigó
- Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Catalonia, Spain
- Programa de Bioinformàtica i Genòmica, Centre de Regulació Genòmica, Barcelona, Catalonia, Spain
- Tel: +34 93 224 0877; Fax: +34 93 224 0875; E-mail:
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48
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Carlson BA, Xu XM, Kryukov GV, Rao M, Berry MJ, Gladyshev VN, Hatfield DL. Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase. Proc Natl Acad Sci U S A 2004; 101:12848-53. [PMID: 15317934 PMCID: PMC516484 DOI: 10.1073/pnas.0402636101] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 1970, a kinase activity that phosphorylated a minor species of seryl-tRNA to form phosphoseryl-tRNA was found in rooster liver [Maenpaa, P. H. & Bernfield, M. R. (1970) Proc. Natl. Acad. Sci. USA 67, 688-695], and a minor seryl-tRNA that decoded the nonsense UGA was detected in bovine liver. The phosphoseryl-tRNA and the minor UGA-decoding seryl-tRNA were subsequently identified as selenocysteine (Sec) tRNA[Ser]Sec, but the kinase activity remained elusive. Herein, by using a comparative genomics approach that searched completely sequenced archaeal genomes for a kinase-like protein with a pattern of occurrence similar to that of components of Sec insertion machinery, we detected a candidate gene for mammalian phosphoseryl-tRNA[Ser]Sec kinase (pstk). Mouse pstk was cloned, and the gene product (PSTK) was expressed and characterized. PSTK specifically phosphorylated the seryl moiety on seryl-tRNA[Ser]Sec and, in addition, had a requirement for ATP and Mg2+. Proteins with homology to mammalian PSTK occur in Drosophila, Caenorhabditis elegans, Methanopyrus kandleri, and Methanococcus jannaschii, suggesting a conservation of its function across archaea and eukaryotes that synthesize selenoproteins and the absence of this function in bacteria, plants, and yeast. The fact that PSTK has been highly conserved in evolution suggests that it plays an important role in selenoprotein biosynthesis and/or regulation.
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Affiliation(s)
- Bradley A Carlson
- Molecular Biology of Selenium Section, Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Development of bioinformatics tools provided researchers with the ability to identify full sets of trace element-containing proteins in organisms for which complete genomic sequences are available. Recently, independent bioinformatics methods were used to identify all, or almost all, genes encoding selenocysteine-containing proteins in human, mouse, and Drosophila genomes, characterizing entire selenoproteomes in these organisms. It also should be possible to search for entire sets of other trace element-associated proteins, such as metal-containing proteins, although methods for their identification are still in development.
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Affiliation(s)
- Vadim N Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA.
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50
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Abstract
In the genetic code, the UGA codon has a dual function as it encodes selenocysteine (Sec) and serves as a stop signal. However, only the translation terminator function is used in gene annotation programs, resulting in misannotation of selenoprotein genes. Here, we applied two independent bioinformatics approaches to characterize a selenoprotein set in prokaryotic genomes. One method searched for selenoprotein genes by identifying RNA stem-loop structures, selenocysteine insertion sequence elements; the second approach identified Sec/Cys pairs in homologous sequences. These analyses identified all or almost all selenoproteins in completely sequenced bacterial and archaeal genomes and provided a view on the distribution and composition of prokaryotic selenoproteomes. In addition, lineage-specific and core selenoproteins were detected, which provided insights into the mechanisms of selenoprotein evolution. Characterization of selenoproteomes allows interpretation of other UGA codons in completed genomes of prokaryotes as terminators, addressing the UGA dual-function problem.
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Affiliation(s)
- Gregory V Kryukov
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
| | - Vadim N Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
- Tel: +1 402 472 4948; Fax: +1 402 472 7842; E-mail:
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