4
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Chan DW, Lam WY, Chen F, Yung MMH, Chan YS, Chan WS, He F, Liu SS, Chan KKL, Li B, Ngan HYS. Genome-wide DNA methylome analysis identifies methylation signatures associated with survival and drug resistance of ovarian cancers. Clin Epigenetics 2021; 13:142. [PMID: 34294135 PMCID: PMC8296615 DOI: 10.1186/s13148-021-01130-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND In contrast to stable genetic events, epigenetic changes are highly plastic and play crucial roles in tumor evolution and development. Epithelial ovarian cancer (EOC) is a highly heterogeneous disease that is generally associated with poor prognosis and treatment failure. Profiling epigenome-wide DNA methylation status is therefore essential to better characterize the impact of epigenetic alterations on the heterogeneity of EOC. METHODS An epigenome-wide association study was conducted to evaluate global DNA methylation in a retrospective cohort of 80 mixed subtypes of primary ovarian cancers and 30 patients with high-grade serous ovarian carcinoma (HGSOC). Three demethylating agents, azacytidine, decitabine, and thioguanine, were tested their anti-cancer and anti-chemoresistant effects on HGSOC cells. RESULTS Global DNA hypermethylation was significantly associated with high-grade tumors, platinum resistance, and poor prognosis. We determined that 9313 differentially methylated probes (DMPs) were enriched in their relative gene regions of 4938 genes involved in small GTPases and were significantly correlated with the PI3K-AKT, MAPK, RAS, and WNT oncogenic pathways. On the other hand, global DNA hypermethylation was preferentially associated with recurrent HGSOC. A total of 2969 DMPs corresponding to 1471 genes were involved in olfactory transduction, and calcium and cAMP signaling. Co-treatment with demethylating agents showed significant growth retardation in ovarian cancer cells through differential inductions, such as cell apoptosis by azacytidine or G2/M cell cycle arrest by decitabine and thioguanine. Notably, azacytidine and decitabine, though not thioguanine, synergistically enhanced cisplatin-mediated cytotoxicity in HGSOC cells. CONCLUSIONS This study demonstrates the significant association of global hypermethylation with poor prognosis and drug resistance in high-grade EOC and highlights the potential of demethylating agents in cancer treatment.
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Affiliation(s)
- David W Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China.
| | - Wai-Yip Lam
- Lee's Pharmaceutical (HK) Ltd, 1/F Building 20E, Phase 3, Hong Kong Science Park, Shatin, Hong Kong, People's Republic of China
| | - Fushun Chen
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Mingo M H Yung
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Yau-Sang Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Wai-Sun Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Fangfang He
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Stephanie S Liu
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Karen K L Chan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China
| | - Benjamin Li
- Lee's Pharmaceutical (HK) Ltd, 1/F Building 20E, Phase 3, Hong Kong Science Park, Shatin, Hong Kong, People's Republic of China
| | - Hextan Y S Ngan
- Department of Obstetrics and Gynaecology, L747 Laboratory Block, LKS Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong, SAR, People's Republic of China. .,Department of Obstetrics and Gynaecology, 6/F Professorial Block, Queen Mary Hospital, Pokfulam, Hong Kong, People's Republic of China.
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10
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Grant DJ, Manichaikul A, Alberg AJ, Bandera EV, Barnholtz‐Sloan J, Bondy M, Cote ML, Funkhouser E, Moorman PG, Peres LC, Peters ES, Schwartz AG, Terry PD, Wang X, Keku TO, Hoyo C, Berchuck A, Sandler DP, Taylor JA, O’Brien KM, Velez Edwards DR, Edwards TL, Beeghly‐Fadiel A, Wentzensen N, Pearce CL, Wu AH, Whittemore AS, McGuire V, Sieh W, Rothstein JH, Modugno F, Ness R, Moysich K, Rossing MA, Doherty JA, Sellers TA, Permuth‐Way JB, Monteiro AN, Levine DA, Setiawan VW, Haiman CA, LeMarchand L, Wilkens LR, Karlan BY, Menon U, Ramus S, Gayther S, Gentry‐Maharaj A, Terry KL, Cramer DW, Goode EL, Larson MC, Kaufmann SH, Cannioto R, Odunsi K, Etter JL, Huang R, Bernardini MQ, Tone AA, May T, Goodman MT, Thompson PJ, Carney ME, Tworoger SS, Poole EM, Lambrechts D, Vergote I, Vanderstichele A, Van Nieuwenhuysen E, Anton‐Culver H, Ziogas A, Brenton JD, Bjorge L, Salvensen HB, Kiemeney LA, Massuger LFAG, Pejovic T, Bruegl A, Moffitt M, Cook L, Le ND, Brooks‐Wilson A, Kelemen LE, Pharoah PD, Song H, Campbell I, Eccles D, DeFazio A, Kennedy CJ, Schildkraut JM. Evaluation of vitamin D biosynthesis and pathway target genes reveals UGT2A1/2 and EGFR polymorphisms associated with epithelial ovarian cancer in African American Women. Cancer Med 2019; 8:2503-2513. [PMID: 31001917 PMCID: PMC6536963 DOI: 10.1002/cam4.1996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/03/2018] [Accepted: 01/08/2019] [Indexed: 02/02/2023] Open
Abstract
An association between genetic variants in the vitamin D receptor (VDR) gene and epithelial ovarian cancer (EOC) was previously reported in women of African ancestry (AA). We sought to examine associations between genetic variants in VDR and additional genes from vitamin D biosynthesis and pathway targets (EGFR, UGT1A, UGT2A1/2, UGT2B, CYP3A4/5, CYP2R1, CYP27B1, CYP24A1, CYP11A1, and GC). Genotyping was performed using the custom-designed 533,631 SNP Illumina OncoArray with imputation to the 1,000 Genomes Phase 3 v5 reference set in 755 EOC cases, including 537 high-grade serous (HGSOC), and 1,235 controls. All subjects are of African ancestry (AA). Logistic regression was performed to estimate odds ratios (OR) and 95% confidence intervals (CI). We further evaluated statistical significance of selected SNPs using the Bayesian False Discovery Probability (BFDP). A significant association with EOC was identified in the UGT2A1/2 region for the SNP rs10017134 (per allele OR = 1.4, 95% CI = 1.2-1.7, P = 1.2 × 10-6 , BFDP = 0.02); and an association with HGSOC was identified in the EGFR region for the SNP rs114972508 (per allele OR = 2.3, 95% CI = 1.6-3.4, P = 1.6 × 10-5 , BFDP = 0.29) and in the UGT2A1/2 region again for rs1017134 (per allele OR = 1.4, 95% CI = 1.2-1.7, P = 2.3 × 10-5 , BFDP = 0.23). Genetic variants in the EGFR and UGT2A1/2 may increase susceptibility of EOC in AA women. Future studies to validate these findings are warranted. Alterations in EGFR and UGT2A1/2 could perturb enzyme efficacy, proliferation in ovaries, impact and mark susceptibility to EOC.
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Affiliation(s)
- Delores J. Grant
- Department of Biological and Biomedical Sciences, Cancer Research ProgramJLC‐Biomedical/Biotechnology Research Institute, North Carolina Central UniversityDurhamNorth Carolina
| | - Ani Manichaikul
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginia
| | - Anthony J. Alberg
- Department of Epidemiology and Biostatistics, Arnold School of Public HealthUniversity of South CarolinaColumbiaSouth Carolina
| | - Elisa V. Bandera
- Department of Population ScienceRutgers Cancer Institute of New JerseyNew BrunswickNew Jersey
| | - Jill Barnholtz‐Sloan
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOhio
| | - Melissa Bondy
- Cancer Prevention and Population Sciences ProgramBaylor College of MedicineHoustonTexas
| | - Michele L. Cote
- Department of Oncology and the Karmanos Cancer Institute Population Studies and Disparities Research ProgramWayne State University School of MedicineDetroitMichigan
| | - Ellen Funkhouser
- Division of Preventive MedicineUniversity of Alabama at BirminghamBirminghamAlabama
| | - Patricia G. Moorman
- Department of Community and Family MedicineDuke University Medical CenterDurhamNorth Carolina
| | - Lauren C. Peres
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginia
| | - Edward S. Peters
- Epidemiology ProgramLouisiana State University Health Sciences Center School of Public HealthNew OrleansLouisisana
| | - Ann G. Schwartz
- Department of Oncology and the Karmanos Cancer Institute Population Studies and Disparities Research ProgramWayne State University School of MedicineDetroitMichigan
| | - Paul D. Terry
- Department of MedicineUniversity of Tennessee Medical Center – KnoxvilleKnoxvilleTennessee
| | - Xin‐Qun Wang
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginia
| | - Temitope O. Keku
- Departments of Medicine and Nutrition, Division of Gastroenterology and HepatologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina
| | - Cathrine Hoyo
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth Carolina
| | - Andrew Berchuck
- Department of Obstetrics and GynecologyDuke University Medical CenterDurhamNorth Carolina
| | - Dale P. Sandler
- Epidemiology Branch, Division of Intramural ResearchNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNorth Carolina
| | - Jack A. Taylor
- Epidemiology Branch, Division of Intramural ResearchNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNorth Carolina
| | - Katie M. O’Brien
- Epidemiology Branch, Division of Intramural ResearchNational Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkNorth Carolina
| | - Digna R. Velez Edwards
- Vanderbilt Epidemiology Center, Center for Human Genetics Research, Department of Obstetrics and GynecologyVanderbilt University Medical CenterNashvilleTennessee
| | - Todd L. Edwards
- Division of Epidemiology, Center for Human Genetics Research, Department of MedicineVanderbilt University Medical CenterNashvilleTennessee
| | - Alicia Beeghly‐Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology CenterInstitute for Medicine and Public Health, Vanderbilt University Medical CenterNashvilleTennessee
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteBethesdaMaryland
| | - Celeste Leigh Pearce
- Department of EpidemiologyUniversity of Michigan School of Public HealthAnn ArborMichigan
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern California Norris Comprehensive Cancer CenterLos AngelesCalifornia
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of MedicineUniversity of Southern California Norris Comprehensive Cancer CenterLos AngelesCalifornia
| | - Alice S. Whittemore
- Department of Health Research and PolicyStanford University School of MedicineStanfordCalifornia
- Department of Biomedical Data ScienceStanford University School of MedicineStanfordCalifornia
| | - Valerie McGuire
- Department of Health Research and PolicyStanford University School of MedicineStanfordCalifornia
| | - Weiva Sieh
- Department of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Joseph H. Rothstein
- Department of Population Health Science and PolicyIcahn School of Medicine at Mount SinaiNew YorkNew York
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Pittsburgh School of MedicinePittsburghPennsylvania
- Department of EpidemiologyUniversity of Pittsburgh Graduate School of Public HealthPittsburghPennsylvania
- Ovarian Cancer Center of Excellence, Womens Cancer Research ProgramMagee‐Womens Research Institute and University of Pittsburgh Cancer InstitutePittsburghPennsylvania
| | - Roberta Ness
- The University of Texas School of Public HealthHoustonTexas
| | - Kirsten Moysich
- Department of Cancer Prevention and ControlRoswell Park Cancer InstituteBuffaloNew York
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health SciencesFred Hutchinson Cancer Research CenterSeattleWashington
- Department of EpidemiologyUniversity of WashingtonSeattleWashington
| | - Jennifer A. Doherty
- Department of Population Health SciencesHuntsman Cancer Institute, University of UtahSalt Lake City, Utah
| | | | | | | | - Douglas A. Levine
- Gynecology Service, Department of SurgeryMemorial Sloan Kettering Cancer CenterNew YorkNew York
- Gynecologic Oncology, Laura and Isaac Pearlmutter Cancer CenterNew York University Langone Medical CenterNew YorkNew York
| | | | - Christopher A. Haiman
- University of Southern California Norris Comprehensive Cancer CenterLos AngelesCalifornia
| | | | - Lynne R. Wilkens
- Cancer Epidemiology ProgramUniversity of Hawaii Cancer CenterHawaii
| | - Beth Y. Karlan
- Women's Cancer ProgramSamuel Oschin Comprehensive Cancer Institute, Cedars‐Sinai Medical CenterLos AngelesCalifornia
| | - Usha Menon
- MRC CTU at UCL, Institute of Clinical Trials and MethodologyUniversity College LondonLondonUK
| | - Susan Ramus
- School of Women's and Children's HealthUniversity of New South WalesNew South WalesAustralia
- The Kinghorn Cancer CentreGarvan Institute of Medical ResearchDarlinghurstNew South WalesAustralia
| | - Simon Gayther
- Center for Cancer Prevention and Translational GenomicsSamuel Oschin Comprehensive Cancer Institute, Cedars‐Sinai Medical CenterLos AngelesCalifornia
- Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCalifornia
| | | | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemiology CenterBrigham and Women's HospitalBostonMassachusetts
- Harvard T. H. Chan School of Public HealthBostonMassauchusetts
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology CenterBrigham and Women's HospitalBostonMassachusetts
- Harvard T. H. Chan School of Public HealthBostonMassauchusetts
| | - Ellen L. Goode
- Department of Health Science Research, Division of EpidemiologyMayo ClinicRochesterMinnesota
| | - Melissa C. Larson
- Department of Health Science Research, Division of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Scott H. Kaufmann
- Departments of Medicine and PharmacologyMayo ClinicRochesterMinnesota
| | - Rikki Cannioto
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population SciencesRoswell Park Cancer InstituteBuffaloNew York
| | - Kunle Odunsi
- Department of Gynecological OncologyRoswell Park Cancer InstituteBuffaloNew York
| | - John L. Etter
- Department of Cancer Prevention and ControlRoswell Park Cancer InstituteBuffaloNew York
| | - Ruea‐Yea Huang
- Center For ImmunotherapyRoswell Park Cancer InstituteBuffaloNew York
| | - Marcus Q. Bernardini
- Division of Gynecologic OncologyPrincess Margaret Hospital, University Health NetworkTorontoOntarioCanada
| | - Alicia A. Tone
- Division of Gynecologic OncologyPrincess Margaret Hospital, University Health NetworkTorontoOntarioCanada
| | - Taymaa May
- Division of Gynecologic OncologyPrincess Margaret Hospital, University Health NetworkTorontoOntarioCanada
| | - Marc T. Goodman
- Cancer Prevention and ControlSamuel Oschin Comprehensive Cancer Institute, Cedars‐Sinai Medical CenterLos AngelesCalifornia
- Department of Biomedical SciencesCommunity and Population Health Research Institute, Cedars‐Sinai Medical CenterLos AngelesCalifornia
| | - Pamela J. Thompson
- Cancer Prevention and ControlSamuel Oschin Comprehensive Cancer Institute, Cedars‐Sinai Medical CenterLos AngelesCalifornia
| | - Michael E. Carney
- Department of Obstetrics and GynecologyJohn A. Burns School of Medicine, University of HawaiiHonoluluHawaii
| | - Shelley S. Tworoger
- Channing Division of Network MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusetts
| | | | - Diether Lambrechts
- Vesalius Research Center, VIBLeuvenBelgium
- Laboratory for Translational Genetics, Department of OncologyUniversity of LeuvenBelgium
| | - Ignace Vergote
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer InstituteUniversity Hospitals LeuvenLeuvenBelgium
| | - Adriaan Vanderstichele
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer InstituteUniversity Hospitals LeuvenLeuvenBelgium
| | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer InstituteUniversity Hospitals LeuvenLeuvenBelgium
| | - Hoda Anton‐Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, Center for Cancer Genetics Research & Prevention, School of MedicineUniversity of California IrvineIrvineCalifornia
| | - Argyrios Ziogas
- Department of EpidemiologyUniversity of California IrvineIrvineCalifornia
| | - James D. Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Line Bjorge
- Department of Gynecology and ObstetricsHaukeland University HospitalBergenNorway
- Centre for Cancer Biomarkers, Department of Clinical ScienceUniversity of BergenBergenNorway
| | - Helga B. Salvensen
- Department of Gynecology and ObstetricsHaukeland University HospitalBergenNorway
- Centre for Cancer Biomarkers, Department of Clinical ScienceUniversity of BergenBergenNorway
| | - Lambertus A. Kiemeney
- Radboud University Medical CenterRadboud Institute for Health SciencesNijmegenNetherlands
| | - Leon F. A. G. Massuger
- Department of Gynaecology, Radboud University Medical CenterRadboud Institute for Molecular Life sciencesNijmegenThe Netherlands
| | - Tanja Pejovic
- Department of Obstetrics & GynecologyOregon Health & Science UniversityPortlandOregon
- Knight Cancer Institute, Oregon Health & Science UniversityPortlandOregon
| | - Amanda Bruegl
- Department of Obstetrics & GynecologyOregon Health & Science UniversityPortlandOregon
- Knight Cancer Institute, Oregon Health & Science UniversityPortlandOregon
| | - Melissa Moffitt
- Department of Obstetrics & GynecologyOregon Health & Science UniversityPortlandOregon
- Knight Cancer Institute, Oregon Health & Science UniversityPortlandOregon
| | - Linda Cook
- Division of Epidemiology and Biostatistics, Department of Internal MedicineUniversity of New MexicoAlbuquerqueNew Mexico
| | - Nhu D. Le
- Cancer Control Research, British Columbia Cancer AgencyVancouverBritish ColumbiaCanada
| | - Angela Brooks‐Wilson
- Canada's Michael Smith Genome Sciences CentreBritish Columbia Cancer AgencyVancouverBritish ColumbiaCanada
- Department of Biomedical Physiology and KinesiologySimon Fraser UniversityBurnabyBritish ColumbiaCanada
| | - Linda E. Kelemen
- Hollings Cancer Center and Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth Carolina
| | - Paul D.P. Pharoah
- Strangeways Research laboratory, Department of Oncology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Honglin Song
- Strangeways Research Laboratory, Department of OncologyUniversity of CambridgeCambridgeUK
| | - Ian Campbell
- Cancer Genetics Laboratory, Research DivisionPeter MacCallum Cancer CentreVictoriaAustralia
- Department of PathologyUniversity of MelbourneParkvilleVictoriaAustralia
| | - Diana Eccles
- Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Anna DeFazio
- Centre for Cancer ResearchThe Westmead Institute for Medical Research, The University of SydneySydneyNew South WalesAustralia
- Department of Gynaecological OncologyWestmead HospitalSydneyNew South WalesAustralia
| | - Catherine J. Kennedy
- Centre for Cancer ResearchThe Westmead Institute for Medical Research, The University of SydneySydneyNew South WalesAustralia
- Department of Gynaecological OncologyWestmead HospitalSydneyNew South WalesAustralia
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16
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Cuellar-Partida G, Lu Y, Dixon SC, Fasching PA, Hein A, Burghaus S, Beckmann MW, Lambrechts D, Van Nieuwenhuysen E, Vergote I, Vanderstichele A, Doherty JA, Rossing MA, Chang-Claude J, Rudolph A, Wang-Gohrke S, Goodman MT, Bogdanova N, Dörk T, Dürst M, Hillemanns P, Runnebaum IB, Antonenkova N, Butzow R, Leminen A, Nevanlinna H, Pelttari LM, Edwards RP, Kelley JL, Modugno F, Moysich KB, Ness RB, Cannioto R, Høgdall E, Høgdall C, Jensen A, Giles GG, Bruinsma F, Kjaer SK, Hildebrandt MAT, Liang D, Lu KH, Wu X, Bisogna M, Dao F, Levine DA, Cramer DW, Terry KL, Tworoger SS, Stampfer M, Missmer S, Bjorge L, Salvesen HB, Kopperud RK, Bischof K, Aben KKH, Kiemeney LA, Massuger LFAG, Brooks-Wilson A, Olson SH, McGuire V, Rothstein JH, Sieh W, Whittemore AS, Cook LS, Le ND, Blake Gilks C, Gronwald J, Jakubowska A, Lubiński J, Kluz T, Song H, Tyrer JP, Wentzensen N, Brinton L, Trabert B, Lissowska J, McLaughlin JR, Narod SA, Phelan C, Anton-Culver H, Ziogas A, Eccles D, Campbell I, Gayther SA, Gentry-Maharaj A, Menon U, Ramus SJ, Wu AH, Dansonka-Mieszkowska A, Kupryjanczyk J, Timorek A, Szafron L, Cunningham JM, Fridley BL, Winham SJ, Bandera EV, Poole EM, Morgan TK, Goode EL, Schildkraut JM, Pearce CL, Berchuck A, Pharoah PDP, Webb PM, Chenevix-Trench G, Risch HA, MacGregor S. Assessing the genetic architecture of epithelial ovarian cancer histological subtypes. Hum Genet 2016; 135:741-56. [PMID: 27075448 PMCID: PMC4976079 DOI: 10.1007/s00439-016-1663-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/24/2016] [Indexed: 10/22/2022]
Abstract
Epithelial ovarian cancer (EOC) is one of the deadliest common cancers. The five most common types of disease are high-grade and low-grade serous, endometrioid, mucinous and clear cell carcinoma. Each of these subtypes present distinct molecular pathogeneses and sensitivities to treatments. Recent studies show that certain genetic variants confer susceptibility to all subtypes while other variants are subtype-specific. Here, we perform an extensive analysis of the genetic architecture of EOC subtypes. To this end, we used data of 10,014 invasive EOC patients and 21,233 controls from the Ovarian Cancer Association Consortium genotyped in the iCOGS array (211,155 SNPs). We estimate the array heritability (attributable to variants tagged on arrays) of each subtype and their genetic correlations. We also look for genetic overlaps with factors such as obesity, smoking behaviors, diabetes, age at menarche and height. We estimated the array heritabilities of high-grade serous disease ([Formula: see text] = 8.8 ± 1.1 %), endometrioid ([Formula: see text] = 3.2 ± 1.6 %), clear cell ([Formula: see text] = 6.7 ± 3.3 %) and all EOC ([Formula: see text] = 5.6 ± 0.6 %). Known associated loci contributed approximately 40 % of the total array heritability for each subtype. The contribution of each chromosome to the total heritability was not proportional to chromosome size. Through bivariate and cross-trait LD score regression, we found evidence of shared genetic backgrounds between the three high-grade subtypes: serous, endometrioid and undifferentiated. Finally, we found significant genetic correlations of all EOC with diabetes and obesity using a polygenic prediction approach.
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Affiliation(s)
- Gabriel Cuellar-Partida
- Statistical Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
- School of Medicine, University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Yi Lu
- Statistical Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Suzanne C Dixon
- Gynaecological Cancers Group, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
- School of Public Health, University of Queensland, Herston, QLD 4006, Australia
| | - Peter A Fasching
- Division of Hematology and Oncology, Department of Medicine, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, USA
- Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Universitaetsstrasse 21-23, 91054, Erlangen, Germany
| | - Alexander Hein
- Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Universitaetsstrasse 21-23, 91054, Erlangen, Germany
| | - Stefanie Burghaus
- Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Universitaetsstrasse 21-23, 91054, Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Universitaetsstrasse 21-23, 91054, Erlangen, Germany
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
- Vesalius Research Center, VIB, Louvain, Belgium
| | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Louvain, Belgium
| | - Ignace Vergote
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Louvain, Belgium
| | - Adriaan Vanderstichele
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Louvain, Belgium
| | - Jennifer Anne Doherty
- Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Mary Anne Rossing
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Community and Population Health Research Institute, Los Angeles, CA, USA
| | - Natalia Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena-University Hospital-Friedrich Schiller University, Jena, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Ingo B Runnebaum
- Department of Gynecology, Jena-University Hospital-Friedrich Schiller University, Jena, Germany
| | | | - Ralf Butzow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Robert P Edwards
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Joseph L Kelley
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Rikki Cannioto
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Graham G Giles
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Karen H Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanny Dao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Meir Stampfer
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stacey Missmer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Reidun K Kopperud
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Katharina Bischof
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Centre for Cancer Biomarkers, University of Bergen, Bergen, Norway
| | - Katja K H Aben
- Radboud University Medical Centre, RADBOUD Institute for Health Sciences, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Lambertus A Kiemeney
- Radboud University Medical Centre, RADBOUD Institute for Health Sciences, Nijmegen, The Netherlands
| | - Leon F A G Massuger
- Department of Obstetrics and Gynaecology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie McGuire
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph H Rothstein
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Weiva Sieh
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alice S Whittemore
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - C Blake Gilks
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Kluz
- Faculty of Medicine, Institute of Midwifery and Emergency Medicine, Clinic of Obstetrics and Gynecology, Frederick Chopin Clinical Provincial Hospital No 1, University of Rzeszów, Rzeszow, Poland
| | - Honglin Song
- Department of Oncology, The Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Department of Oncology, The Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | | | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, ON, Canada
| | - Catherine Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
- Center for Cancer Genetics Research and Prevention, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ian Campbell
- Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Australia
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | - Usha Menon
- Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Agnieszka Timorek
- Department of Obstetrics, Gynaecology and Oncology, IInd Faculty of Medicine, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Lukasz Szafron
- Department of Pathology and Laboratory Diagnostics, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Julie M Cunningham
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Brooke L Fridley
- Department of Biostatistics, University of Kansas, Kansas City, KS, USA
| | - Stacey J Winham
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Terry K Morgan
- Department of Pathology and Obstetrics, OHSU, Portland, OR, USA
- Department of Gynaecology, OHSU, Portland, OR, USA
| | - Ellen L Goode
- Division of Epidemiology, Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | | | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Andrew Berchuck
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, The Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, The Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Penelope M Webb
- Gynaecological Cancers Group, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
- School of Public Health, University of Queensland, Herston, QLD 4006, Australia
| | - Georgia Chenevix-Trench
- Cancer Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
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