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Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 2016; 29:723-736. [PMID: 27165744 PMCID: PMC4864952 DOI: 10.1016/j.ccell.2016.04.002] [Citation(s) in RCA: 375] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/08/2015] [Accepted: 04/05/2016] [Indexed: 01/08/2023]
Abstract
We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.
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Affiliation(s)
- Siyuan Zheng
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ninad Dewal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Moffitt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ludmila Danilova
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Bradley A Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Antonio M Lerario
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tobias Else
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Rue du Bugnon 27, 1005 Lausanne, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Seungchan Kim
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Guillaume Assie
- Inserm U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France; Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Department of Endocrinology, Referral Center for Rare Adrenal Diseases, Assistance Publique Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France; European Network for the Study of Adrenal Tumors, 75014 Paris, France
| | - Olena Morozova
- University of California Santa Cruz Genomics Institute, University California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jens Waldmann
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Department of Visceral, Thoracic and Vascular Surgery, University Hospital Giessen and Marburg, Campus Marburg, General Surgery, Endocrine Center, 34501 Marburg, Germany
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Hsin-Ta Wu
- Department of Computer Science, Brown University, Providence, RI 02906, USA
| | - Benjamin J Raphael
- Department of Computer Science, Brown University, Providence, RI 02906, USA
| | - Lina Shao
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Harvard Medical School, Boston, MA 02215, USA
| | | | - Felix Beuschlein
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Endocrine Research Unit, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, 80336 Munich, Germany
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group and Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2006, Australia; Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Stan B Sidhu
- Cancer Diagnosis and Pathology Group and Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2006, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Madson Q Almeida
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Maria C B V Fragoso
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Leslie M Cope
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Electron Kebebew
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mouhammed A Habra
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kimberly J Bussey
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA; NantOmics, LLC, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5001, USA
| | - William E Rainey
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sylvia L Asa
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Jérôme Bertherat
- Inserm U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France; Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Department of Endocrinology, Referral Center for Rare Adrenal Diseases, Assistance Publique Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France; European Network for the Study of Adrenal Tumors, 75014 Paris, France
| | - Martin Fassnacht
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Endocrine and Diabetes Unit, Department of Internal Medicine I, University Hospital Würzburg, 97080 Würzburg, Germany; Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gary D Hammer
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas J Giordano
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Roel G W Verhaak
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Kim JT, Li J, Jang ER, Gulhati P, Rychahou PG, Napier DL, Wang C, Weiss HL, Lee EY, Anthony L, Townsend CM, Liu C, Evers B. Deregulation of Wnt/β-catenin signaling through genetic or epigenetic alterations in human neuroendocrine tumors. Carcinogenesis 2013; 34:953-61. [PMID: 23354304 PMCID: PMC3643417 DOI: 10.1093/carcin/bgt018] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/19/2012] [Accepted: 01/12/2013] [Indexed: 12/18/2022] Open
Abstract
Carcinoid tumors are rare neuroendocrine tumors (NETs) that are increasing in incidence. Mutation and altered expression of Wnt/β-catenin signaling components have been described in many tumors but have not been well-studied in NETs. Here, we observed accumulation of β-catenin in the cytoplasm and/or nucleus in 25% of clinical NET tissues. By mutational analysis, the mutations of β-catenin (I35S) and APC (E1317Q, T1493T) were identified in NET cells and the tissues. Expression of representative Wnt inhibitors was absent or markedly decreased in BON, a human pancreatic carcinoid cell line; treatment with 5-aza-2'-deoxycytidine (5-aza-CdR) increased expression levels of the Wnt inhibitors. Methylation analyses demonstrated that CpG islands of SFRP-1 and Axin-2 were methylated, whereas the promoters of DKK-1, DKK-3 and WIF-1 were unmethylated in four NET cells. Aberrant methylation of SFRP-1 was particularly observed in most of clinical NET tissues. In addition, the repression of these unmethylated genes was associated with histone H3 lysine 9 dimethylation (H3K9me2) in BON cells. Together, 5-aza-CdR treatment inhibited cell proliferation and decreased the protein levels of H3K9me2 and G9a. Moreover, a novel G9a inhibitor, UNC0638, suppressed BON cell proliferation through inhibition of Wnt/β-catenin pathway. Overexpression of the inhibitory genes, particularly SFRP-1 and WIF-1 in BON cells, resulted in suppression of anchorage-independent growth and inhibition of tumor growth in mice. Our findings suggest that aberrant Wnt/β-catenin signaling, through either mutations or epigenetic silencing of Wnt antagonists, contributes to the pathogenesis and growth of NETs and have important clinical implications for the prognosis and treatment of NETs.
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Affiliation(s)
- Ji Tae Kim
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Jing Li
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Eun Ryoung Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Pat Gulhati
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Surgery, University of Kentucky, Lexington, KY, USA
- MD/PhD Program, University of Texas Medical Branch, Galveston, TX, USA
| | - Piotr G. Rychahou
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Surgery, University of Kentucky, Lexington, KY, USA
| | - Dana L. Napier
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Heidi L. Weiss
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Eun Y. Lee
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Lowell Anthony
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA and
| | | | - Chunming Liu
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - B.Mark Evers
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
- Department of Surgery, University of Kentucky, Lexington, KY, USA
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7
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Wong HL, Peters U, Hayes RB, Huang WY, Schatzkin A, Bresalier RS, Velie EM, Brody LC. Polymorphisms in the adenomatous polyposis coli (APC) gene and advanced colorectal adenoma risk. Eur J Cancer 2010; 46:2457-66. [PMID: 20510605 PMCID: PMC2924917 DOI: 10.1016/j.ejca.2010.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 04/14/2010] [Accepted: 04/20/2010] [Indexed: 02/07/2023]
Abstract
While germline mutations in the adenomatous polyposis coli (APC) gene cause the hereditary colon cancer syndrome (familial adenomatous polyposis (FAP)), the role of common germline APC variants in sporadic adenomatous polyposis remains unclear. We studied the association of eight APC single nucleotide polymorphisms (SNPs), possibly associated with functional consequences, and previously identified gene-environment (dietary fat intake and hormone replacement therapy (HRT) use) interactions, in relation to advanced colorectal adenoma in 758 cases and 767 sex- and race-matched controls, randomly selected from the screening arm of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Cases had at least one verified advanced adenoma of the distal colon; controls, a negative sigmoidoscopy. We did not observe an association between genotypes for any of the eight APC SNPs and advanced distal adenoma risk (P(global gene-based)=0.92). Frequencies of identified common haplotypes did not differ between cases and controls (P(global haplotype test)=0.97). However, the risk for advanced distal adenoma was threefold higher for one rare haplotype (cases: 2.7%; controls: 1.6%) (odds ratio (OR)=3.27; 95% confidence interval (CI)=1.08-9.88). The genetic association between D1822V and advanced distal adenoma was confined to persons consuming a high-fat diet (P(interaction)=0.03). Similar interactions were not observed with HRT use. In our large, nested case-control study of advanced distal adenoma and clinically verified adenoma-free controls, we observed no association between specific APC SNPs and advanced adenoma. Fat intake modified the APC D1822V-adenoma association, but further studies are warranted.
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Affiliation(s)
- Hui-Lee Wong
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Ulrike Peters
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
- Cancer Prevention Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Richard B. Hayes
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Wen-Yi Huang
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Arthur Schatzkin
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Robert S. Bresalier
- Department of Gastrointestinal Medicine and Nutrition, M.D. Anderson Cancer Center, Houston, TX
| | - Ellen M. Velie
- Department of Epidemiology, Michigan State University, East Lansing, MI
| | - Lawrence C. Brody
- Department of Health and Human Services, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, NIH, Bethesda MD
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