1
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Yang Y, Chen Y, Xu S, Guo X, Jia G, Ping J, Shu X, Zhao T, Yuan F, Wang G, Xie Y, Ci H, Liu H, Qi Y, Liu Y, Liu D, Li W, Ye F, Shu XO, Zheng W, Li L, Cai Q, Long J. Integrating muti-omics data to identify tissue-specific DNA methylation biomarkers for cancer risk. Nat Commun 2024; 15:6071. [PMID: 39025880 PMCID: PMC11258330 DOI: 10.1038/s41467-024-50404-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The relationship between tissue-specific DNA methylation and cancer risk remains inadequately elucidated. Leveraging resources from the Genotype-Tissue Expression consortium, here we develop genetic models to predict DNA methylation at CpG sites across the genome for seven tissues and apply these models to genome-wide association study data of corresponding cancers, namely breast, colorectal, renal cell, lung, ovarian, prostate, and testicular germ cell cancers. At Bonferroni-corrected P < 0.05, we identify 4248 CpGs that are significantly associated with cancer risk, of which 95.4% (4052) are specific to a particular cancer type. Notably, 92 CpGs within 55 putative novel loci retain significant associations with cancer risk after conditioning on proximal signals identified by genome-wide association studies. Integrative multi-omics analyses reveal 854 CpG-gene-cancer trios, suggesting that DNA methylation at 309 distinct CpGs might influence cancer risk through regulating the expression of 205 unique cis-genes. These findings substantially advance our understanding of the interplay between genetics, epigenetics, and gene expression in cancer etiology.
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Affiliation(s)
- Yaohua Yang
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA.
| | - Yaxin Chen
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shuai Xu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tianying Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fangcheng Yuan
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gang Wang
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yufang Xie
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hang Ci
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hongmo Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yawen Qi
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Dan Liu
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Institute of Respiratory Health, Frontiers Science Center for Disease‑Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Li Li
- Department of Family Medicine, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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2
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Coetzee SG, Hazelett DJ. MotifbreakR v2: extended capability and database integration. ARXIV 2024:arXiv:2407.03441v1. [PMID: 39010878 PMCID: PMC11247919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor suite of software packages and annotations to operate across a diverse array of genomes and motif databases. Initially developed to interrogate the effect of single nucleotide variants (common and rare SNVs) on potential TF binding sites, in motifbreakR v2, we have updated the functionality. New features include the ability to query other types of more complex genetic variants, such as short insertions and deletions (indels). This function allows modeling a more extensive array of variants that may have more significant effects on TF binding. Additionally, while TF binding is based partly on sequence preference, predictions of TF binding based on sequence preference alone can indicate many more potential binding events than observed. Adding information from DNA-binding sequencing datasets lends confidence to motif disruption prediction by demonstrating TF binding in cell lines and tissue types. Therefore, motifbreakR implements querying the ReMap2022 database for evidence that a TF matching the disrupted motif binds over the disrupting variant. Finally, in motifbreakR, in addition to the existing interface, we have implemented an R/Shiny graphical user interface to simplify and enhance access to researchers with different skill sets.
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Affiliation(s)
- Simon G Coetzee
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
| | - Dennis J Hazelett
- Department of Computational Biomedicine at Cedars-Sinai Medical Center
- Cancer Prevention and Control - Samuel Oschin Cancer Center, Cedars-Sinai
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3
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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie JL, Aeilts AM, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 Germline Variants with TP53 Somatic Variants in Breast Tumors in a Genome-wide Study. CANCER RESEARCH COMMUNICATIONS 2024; 4:1597-1608. [PMID: 38836758 PMCID: PMC11210444 DOI: 10.1158/2767-9764.crc-24-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/16/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. A genome-wide association study was conducted in 2,850 women of European ancestry with breast cancer using TP53 and PIK3CA mutation status (positive or negative) as well as specific functional categories [e.g., TP53 gain-of-function (GOF) and loss-of-function, PIK3CA activating] as phenotypes. Germline variants showing evidence of association were selected for validation analyses and tested in multiple independent datasets. Discovery association analyses found five variants associated with TP53 mutation status with P values <1 × 10-6 and 33 variants with P values <1 × 10-5. Forty-four variants were associated with PIK3CA mutation status with P values <1 × 10-5. In validation analyses, only variants at the ESR1 locus were associated with TP53 mutation status after multiple comparisons corrections. Combined analyses in European and Malaysian populations found ESR1 locus variants rs9383938 and rs9479090 associated with the presence of TP53 mutations overall (P values 2 × 10-11 and 4.6 × 10-10, respectively). rs9383938 also showed association with TP53 GOF mutations (P value 6.1 × 10-7). rs9479090 showed suggestive evidence (P value 0.02) for association with TP53 mutation status in African ancestry populations. No other variants were significantly associated with TP53 or PIK3CA mutation status. Larger studies are needed to confirm these findings and determine if additional variants contribute to ancestry-specific differences in mutation frequency. SIGNIFICANCE Emerging data show ancestry-specific differences in TP53 and PIK3CA mutation frequency in breast tumors suggesting that germline variants may influence somatic mutational processes. This study identified variants near ESR1 associated with TP53 mutation status and identified additional loci with suggestive association which may provide biological insight into observed differences.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, New York
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Medical School, Columbus, Ohio
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, Ohio
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Amber M. Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, Ohio
| | - Heather Hampel
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Integrative Translational Sciences, City of Hope, Duarte, California
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Patrick Stevens
- Bioinformatics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Paolo Fadda
- Genomics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur, Malaysia
| | - Joseph Paul McElroy
- Department of Biomedical Informatics, The Ohio State University Center for Biostatistics, Columbus, Ohio
| | - Amanda E. Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, Ohio
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4
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Iñiguez-Muñoz S, Llinàs-Arias P, Ensenyat-Mendez M, Bedoya-López AF, Orozco JIJ, Cortés J, Roy A, Forsberg-Nilsson K, DiNome ML, Marzese DM. Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements. Cell Mol Life Sci 2024; 81:274. [PMID: 38902506 DOI: 10.1007/s00018-024-05314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/07/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024]
Abstract
Discoveries in the field of genomics have revealed that non-coding genomic regions are not merely "junk DNA", but rather comprise critical elements involved in gene expression. These gene regulatory elements (GREs) include enhancers, insulators, silencers, and gene promoters. Notably, new evidence shows how mutations within these regions substantially influence gene expression programs, especially in the context of cancer. Advances in high-throughput sequencing technologies have accelerated the identification of somatic and germline single nucleotide mutations in non-coding genomic regions. This review provides an overview of somatic and germline non-coding single nucleotide alterations affecting transcription factor binding sites in GREs, specifically involved in cancer biology. It also summarizes the technologies available for exploring GREs and the challenges associated with studying and characterizing non-coding single nucleotide mutations. Understanding the role of GRE alterations in cancer is essential for improving diagnostic and prognostic capabilities in the precision medicine era, leading to enhanced patient-centered clinical outcomes.
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Affiliation(s)
- Sandra Iñiguez-Muñoz
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Miquel Ensenyat-Mendez
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Andrés F Bedoya-López
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain
| | - Javier I J Orozco
- Saint John's Cancer Institute, Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quiron Group, 08017, Barcelona, Spain
- Medica Scientia Innovation Research SL (MEDSIR), 08018, Barcelona, Spain
- Faculty of Biomedical and Health Sciences, Department of Medicine, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- University of Nottingham Biodiscovery Institute, Nottingham, UK
| | - Maggie L DiNome
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Diego M Marzese
- Cancer Epigenetics Laboratory at the Cancer Cell Biology Group, Institut d'Investigació Sanitària Illes Balears (IdISBa), Palma, Spain.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
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5
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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWASs of breast and ovarian cancer identify more than 100 susceptibility genes in the BCAC and OCAC consortia. Am J Hum Genet 2024; 111:1084-1099. [PMID: 38723630 PMCID: PMC11179407 DOI: 10.1016/j.ajhg.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Transcriptome-wide association studies (TWASs) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have focused on the regulatory effects of risk-associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWASs of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole-genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents an in-depth look into the role of trans eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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6
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Dareng EO, Coetzee SG, Tyrer JP, Peng PC, Rosenow W, Chen S, Davis BD, Dezem FS, Seo JH, Nameki R, Reyes AL, Aben KKH, Anton-Culver H, Antonenkova NN, Aravantinos G, Bandera EV, Beane Freeman LE, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bernardini MQ, Bjorge L, Black A, Bogdanova NV, Bolton KL, Brenton JD, Budzilowska A, Butzow R, Cai H, Campbell I, Cannioto R, Chang-Claude J, Chanock SJ, Chen K, Chenevix-Trench G, Chiew YE, Cook LS, DeFazio A, Dennis J, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles DM, Ene G, Fasching PA, Flanagan JM, Fortner RT, Fostira F, Gentry-Maharaj A, Giles GG, Goodman MT, Gronwald J, Haiman CA, Håkansson N, Heitz F, Hildebrandt MAT, Høgdall E, Høgdall CK, Huang RY, Jensen A, Jones ME, Kang D, Karlan BY, Karnezis AN, Kelemen LE, Kennedy CJ, Khusnutdinova EK, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Labrie M, Lambrechts D, Larson MC, Le ND, Lester J, Li L, Lubiński J, Lush M, Marks JR, Matsuo K, May T, McLaughlin JR, McNeish IA, Menon U, Missmer S, Modugno F, Moffitt M, Monteiro AN, Moysich KB, Narod SA, Nguyen-Dumont T, Odunsi K, Olsson H, Onland-Moret NC, Park SK, Pejovic T, Permuth JB, Piskorz A, Prokofyeva D, Riggan MJ, Risch HA, Rodríguez-Antona C, Rossing MA, Sandler DP, Setiawan VW, Shan K, Song H, Southey MC, Steed H, Sutphen R, Swerdlow AJ, Teo SH, Terry KL, Thompson PJ, Vestrheim Thomsen LC, Titus L, Trabert B, Travis R, Tworoger SS, Valen E, Van Nieuwenhuysen E, Edwards DV, Vierkant RA, Webb PM, Weinberg CR, Weise RM, Wentzensen N, White E, Winham SJ, Wolk A, Woo YL, Wu AH, Yan L, Yannoukakos D, Zeinomar N, Zheng W, Ziogas A, Berchuck A, Goode EL, Huntsman DG, Pearce CL, Ramus SJ, Sellers TA, Freedman ML, Lawrenson K, Schildkraut JM, Hazelett D, Plummer JT, Kar S, Jones MR, Pharoah PDP, Gayther SA. Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions. Am J Hum Genet 2024; 111:1061-1083. [PMID: 38723632 PMCID: PMC11179261 DOI: 10.1016/j.ajhg.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 06/07/2024] Open
Abstract
To identify credible causal risk variants (CCVs) associated with different histotypes of epithelial ovarian cancer (EOC), we performed genome-wide association analysis for 470,825 genotyped and 10,163,797 imputed SNPs in 25,981 EOC cases and 105,724 controls of European origin. We identified five histotype-specific EOC risk regions (p value <5 × 10-8) and confirmed previously reported associations for 27 risk regions. Conditional analyses identified an additional 11 signals independent of the primary signal at six risk regions (p value <10-5). Fine mapping identified 4,008 CCVs in these regions, of which 1,452 CCVs were located in ovarian cancer-related chromatin marks with significant enrichment in active enhancers, active promoters, and active regions for CCVs from each EOC histotype. Transcriptome-wide association and colocalization analyses across histotypes using tissue-specific and cross-tissue datasets identified 86 candidate susceptibility genes in known EOC risk regions and 32 genes in 23 additional genomic regions that may represent novel EOC risk loci (false discovery rate <0.05). Finally, by integrating genome-wide HiChIP interactome analysis with transcriptome-wide association study (TWAS), variant effect predictor, transcription factor ChIP-seq, and motifbreakR data, we identified candidate gene-CCV interactions at each locus. This included risk loci where TWAS identified one or more candidate susceptibility genes (e.g., HOXD-AS2, HOXD8, and HOXD3 at 2q31) and other loci where no candidate gene was identified (e.g., MYC and PVT1 at 8q24) by TWAS. In summary, this study describes a functional framework and provides a greater understanding of the biological significance of risk alleles and candidate gene targets at EOC susceptibility loci identified by a genome-wide association study.
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Affiliation(s)
- Eileen O Dareng
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Simon G Coetzee
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pei-Chen Peng
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Will Rosenow
- 3Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brian D Davis
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe Segato Dezem
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robbin Nameki
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alberto L Reyes
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Katja K H Aben
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Netherlands Comprehensive Cancer Organisation, Utrecht, the Netherlands
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | | | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Line Bjorge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amanda Black
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus; Department of Radiation Oncology, Hannover Medical School, Hannover, Germany; Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Kelly L Bolton
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO, USA
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Agnieszka Budzilowska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ralf Butzow
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Center, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rikki Cannioto
- Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Kexin Chen
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Yoke-Eng Chiew
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Linda S Cook
- Epidemiology, School of Public Health, University of Colorado, Aurora, CO, USA; Community Health Sciences, University of Calgary, Calgary, AB, Canada
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia; The Daffodil Centre, a joint venture with Cancer Council NSW, The University of Sydney, Sydney, NSW, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecological Oncology; HSK, Dr. Horst-Schmidt Klinik, Wiesbaden, Wiesbaden, Germany; Department of Gynecology and Gynecologic Oncology, Evangelische Kliniken Essen-Mitte (KEM), Essen, Germany
| | - Matthias Dürst
- Department of Gynaecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gabrielle Ene
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany
| | - James M Flanagan
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Marc T Goodman
- Cancer Prevention and Control Program, Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Florian Heitz
- Department of Gynecology and Gynecological Oncology; HSK, Dr. Horst-Schmidt Klinik, Wiesbaden, Wiesbaden, Germany; Department of Gynecology and Gynecologic Oncology, Evangelische Kliniken Essen-Mitte (KEM), Essen, Germany; Center for Pathology, Evangelische Kliniken Essen-Mitte, Essen, Germany
| | | | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K Høgdall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ruea-Yea Huang
- Center For Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Linda E Kelemen
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Catherine J Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia; The University of Sydney, Sydney, NSW, Australia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia; Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Lambertus A Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K Kjaer
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marilyne Labrie
- Department of Immunology and Cell Biology, FMSS - Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Nhu D Le
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Lian Li
- Department of Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jeffrey R Marks
- Department of Surgery, Duke University Hospital, Durham, NC, USA
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - John R McLaughlin
- Public Health Ontario, Samuel Lunenfeld Research Institute, Toronto, ON, Canada
| | - Iain A McNeish
- Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, Imperial College London, London, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Usha Menon
- MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Stacey Missmer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Francesmary Modugno
- Women's Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Melissa Moffitt
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Steven A Narod
- Women's College Research Institute, University of Toronto, Toronto, ON, Canada
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA; Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL, USA
| | - Håkan Olsson
- Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Utrecht, UMC Utrecht, Utrecht, the Netherlands
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea; Cancer Research Institute, Seoul National University, Seoul, Korea; Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, South Korea
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Marjorie J Riggan
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Cristina Rodríguez-Antona
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - V Wendy Setiawan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kang Shan
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Honglin Song
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Helen Steed
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada; Section of Gynecologic Oncology Surgery, Alberta Health Services, North Zone, Edmonton, AB, Canada
| | - Rebecca Sutphen
- Epidemiology Center, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia; Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kathryn L Terry
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics and Gyneoclogy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Pamela J Thompson
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Liv Cecilie Vestrheim Thomsen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Linda Titus
- Muskie School of Public Service, University of Southern Maine, Portland, ME, USA
| | - Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ruth Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Shelley S Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Ellen Valen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway; Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Els Van Nieuwenhuysen
- Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Leuven, Belgium
| | - Digna Velez Edwards
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Women's Health Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert A Vierkant
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Penelope M Webb
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Rayna Matsuno Weise
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Emily White
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, University of Malaya Medical Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Li Yan
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Nur Zeinomar
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, CA, USA
| | - Andrew Berchuck
- Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - David G Huntsman
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada
| | - 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
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine and Health, University of NSW Sydney, Sydney, NSW, Australia; Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, NSW, Australia
| | | | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Lawrenson
- Women's Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dennis Hazelett
- Samuel Oschin Comprehensive Cancer Institute, The Center for Bioinformatics and Functional Biology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jasmine T Plummer
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michelle R Jones
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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7
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Li Q, Song Q, Chen Z, Choi J, Moreno V, Ping J, Wen W, Li C, Shu X, Yan J, Shu XO, Cai Q, Long J, Huyghe JR, Pai R, Gruber SB, Casey G, Wang X, Toriola AT, Li L, Singh B, Lau KS, Zhou L, Wu C, Peters U, Zheng W, Long Q, Yin Z, Guo X. Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention and intervention. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308170. [PMID: 38853880 PMCID: PMC11160851 DOI: 10.1101/2024.05.29.24308170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Identifying risk protein targets and their therapeutic drugs is crucial for effective cancer prevention. Here, we conduct integrative and fine-mapping analyses of large genome-wide association studies data for breast, colorectal, lung, ovarian, pancreatic, and prostate cancers, and characterize 710 lead variants independently associated with cancer risk. Through mapping protein quantitative trait loci (pQTL) for these variants using plasma proteomics data from over 75,000 participants, we identify 365 proteins associated with cancer risk. Subsequent colocalization analysis identifies 101 proteins, including 74 not reported in previous studies. We further characterize 36 potential druggable proteins for cancers or other disease indications. Analyzing >3.5 million electronic health records, we uncover five drugs (Haloperidol, Trazodone, Tranexamic Acid, Haloperidol, and Captopril) associated with increased cancer risk and two drugs (Caffeine and Acetazolamide) linked to reduced colorectal cancer risk. This study offers novel insights into therapeutic drugs targeting risk proteins for cancer prevention and intervention.
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8
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Xing T, Zhao Y, Wang L, Geng W, Liu W, Zhou J, Huang C, Wang W, Chu X, Liu B, Chen K, Zheng H, Li L. Fine-scale mapping of chromosome 9q22.33 identifies candidate causal variant in ovarian cancer. PeerJ 2024; 12:e16918. [PMID: 38371376 PMCID: PMC10874173 DOI: 10.7717/peerj.16918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Ovarian cancer is a complex polygenic disease in which genetic factors play a significant role in disease etiology. A genome-wide association study (GWAS) identified a novel variant on chromosome 9q22.33 as a susceptibility locus for epithelial ovarian cancer (EOC) in the Han Chinese population. However, the underlying mechanism of this genomic region remained unknown. In this study, we conducted a fine-mapping analysis of 130 kb regions, including 1,039 variants in 200 healthy women. Ten variants were selected to evaluate the association with EOC risk in 1,099 EOC cases and 1,591 controls. We identified two variants that were significantly associated with ovarian cancer risk (rs7027650, P = 1.91 × 10-7; rs1889268, P = 3.71 × 10-2). Expression quantitative trait locus (eQTL) analysis found that rs7027650 was significantly correlated with COL15A1 gene expression (P = 0.009). The Luciferase reporter gene assay confirmed that rs7027650 could interact with the promoter region of COL15A1, reducing its activity. An electrophoretic mobility shift assay (EMSA) showed the allele-specific binding capacity of rs7027650. These findings revealed that rs7027650 could be a potential causal variant at 9q22.33 region and may regulate the expression level of COL15A1. This study offered insight into the molecular mechanism behind a potential causal variant that affects the risk of ovarian cancer.
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Affiliation(s)
- Tongyu Xing
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lili Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Geng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jingjing Zhou
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Caiyun Huang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Human Major Diseases, Ministry of Education, Tianjin’s Clinical Research Center for Cancer, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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9
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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie J, Aeilts A, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 germline variants with TP53 somatic variants in breast tumors in a genome-wide study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299442. [PMID: 38106140 PMCID: PMC10723566 DOI: 10.1101/2023.12.06.23299442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of TP53 somatic mutations than other subtypes. PIK3CA mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. Methods A genome-wide association study was conducted using breast cancer mutation status of TP53 and PIK3CA and functional mutation categories including TP53 gain of function (GOF) and loss of function mutations and PIK3CA activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC. Results The discovery Germline x Mutation (GxM) association study found five variants associated with one or more TP53 phenotypes with P values <1×10-6, 33 variants associated with one or more TP53 phenotypes with P values <1×10-5, and 44 variants associated with one or more PIK3CA phenotypes with P values <1×10-5. In the multi-ancestry and Malaysian validation studies, germline ESR1 locus variant, rs9383938, was associated with the presence of TP53 mutations overall (P values 6.8×10-5 and 9.8×10-8, respectively) and TP53 GOF mutations (P value 8.4×10-6). Multiple variants showed suggestive evidence of association with PIK3CA mutation status in the validation studies, but none were significant after correction for multiple comparisons. Conclusions We found evidence that germline variants were associated with TP53 and PIK3CA mutation status in breast cancers. Variants near the estrogen receptor alpha gene, ESR1, were significantly associated with overall TP53 mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, NY, USA
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Medical School, Columbus, OH, 43210, USA
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, OH 43210, USA
| | - Susan L. Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Elad Ziv
- University of California, Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- University of California, Department of Medicine, San Francisco, San Francisco, CA, USA
- University of California San Francisco, Institute for Human Genetics, San Francisco, CA, USA
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jessica Gillespie
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Amber Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Heather Hampel
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Integrative Translational Sciences, City of Hope, Duarte, CA
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Patrick Stevens
- The Ohio State University Comprehensive Cancer Center, Bioinformatics Shared Resource, Columbus, OH, USA
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Paolo Fadda
- The Ohio State University Comprehensive Cancer Center, Genomics Shared Resource, Columbus, OH, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Joseph Paul McElroy
- The Ohio State University Center for Biostatistics, Department of Biomedical Informatics, Columbus, OH, USA
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWAS of breast and ovarian cancer identify more than 100 risk associated genes in the BCAC and OCAC consortia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566218. [PMID: 38014246 PMCID: PMC10680675 DOI: 10.1101/2023.11.09.566218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Transcriptome-wide association studies (TWAS) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have only considered regulatory effects of risk associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWAS of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents a first look into the role of trans-eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S. Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P. Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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11
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Haycock PC, Borges MC, Burrows K, Lemaitre RN, Harrison S, Burgess S, Chang X, Westra J, Khankari NK, Tsilidis KK, Gaunt T, Hemani G, Zheng J, Truong T, O’Mara TA, Spurdle AB, Law MH, Slager SL, Birmann BM, Saberi Hosnijeh F, Mariosa D, Amos CI, Hung RJ, Zheng W, Gunter MJ, Davey Smith G, Relton C, Martin RM. Design and quality control of large-scale two-sample Mendelian randomization studies. Int J Epidemiol 2023; 52:1498-1521. [PMID: 38587501 PMCID: PMC10555669 DOI: 10.1093/ije/dyad018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/10/2023] [Indexed: 03/27/2024] Open
Abstract
Background Mendelian randomization (MR) studies are susceptible to metadata errors (e.g. incorrect specification of the effect allele column) and other analytical issues that can introduce substantial bias into analyses. We developed a quality control (QC) pipeline for the Fatty Acids in Cancer Mendelian Randomization Collaboration (FAMRC) that can be used to identify and correct for such errors. Methods We collated summary association statistics from fatty acid and cancer genome-wide association studies (GWAS) and subjected the collated data to a comprehensive QC pipeline. We identified metadata errors through comparison of study-specific statistics to external reference data sets (the National Human Genome Research Institute-European Bioinformatics Institute GWAS catalogue and 1000 genome super populations) and other analytical issues through comparison of reported to expected genetic effect sizes. Comparisons were based on three sets of genetic variants: (i) GWAS hits for fatty acids, (ii) GWAS hits for cancer and (iii) a 1000 genomes reference set. Results We collated summary data from 6 fatty acid and 54 cancer GWAS. Metadata errors and analytical issues with the potential to introduce substantial bias were identified in seven studies (11.6%). After resolving metadata errors and analytical issues, we created a data set of 219 842 genetic associations with 90 cancer types, generated in analyses of 566 665 cancer cases and 1 622 374 controls. Conclusions In this large MR collaboration, 11.6% of included studies were affected by a substantial metadata error or analytical issue. By increasing the integrity of collated summary data prior to their analysis, our protocol can be used to increase the reliability of downstream MR analyses. Our pipeline is available to other researchers via the CheckSumStats package (https://github.com/MRCIEU/CheckSumStats).
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Affiliation(s)
- Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Sean Harrison
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Xuling Chang
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat—National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Jason Westra
- Department of Mathematics, Statistics, and Computer Science, Dordt College, Sioux Center, IA, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kostas K Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
| | - Tom Gaunt
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Therese Truong
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Team “Exposome, Heredity, Cancer and Health”, CESP, Villejuif, France
| | - Tracy A O’Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Daniela Mariosa
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christopher I Amos
- Dan L Duncan Comprehensive Cancer Center Baylor College of Medicine, Houston, USA
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health and University of Toronto, Toronto, Canada
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marc J Gunter
- Section of Nutrition and Metabolism, International Agency for Research on Cancer (IARC), Lyon, France
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Biomedical Research Centre at University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
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12
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Wang XC, Zhou H, Jiang WJ, Jiang P, Sun YC, Ni WJ. Effect of CX3CL1/CX3CR1 gene polymorphisms on the clinical efficacy of carboplatin therapy in Han patients with ovarian cancer. Front Genet 2023; 13:1065213. [PMID: 36685881 PMCID: PMC9852718 DOI: 10.3389/fgene.2022.1065213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Gene polymorphisms have a close relationship with the clinical effects of carboplatin for ovarian cancer. Here, we investigated the relationship between CX3CL1 and CX3CR1 genotypes and the clinical efficacy of carboplatin in ovarian cancer, thereby clarifying the unidentified genetic factors that influence the efficacy of carboplatin in ovarian cancer. Based on the above purposes, we used Sequenom Mass ARRAY technology to detect CX3CL1 and CX3CR1 gene polymorphisms in 127 patients with carboplatin-treated ovarian cancer. We performed various statistical analyses to evaluate the effects of CX3CL1 and CX3CR1 genetic variants, demographic data, and clinical characteristics on the effect of carboplatin therapy. The results show that the CX3CL1 genotypes rs223815 (G>C) and rs682082 (G>A) will significantly affect the clinical efficacy of carboplatin for ovarian cancer (p < 0.05), while the other six genotypes and all CX3CR1 genotypes have no significant effect (p > 0.05). In addition, only one population factor, age, had a significant effect on the clinical efficacy of carboplatin-treated ovarian cancer (p < 0.05). Based on the above research results, we concluded that the clinical efficacy of carboplatin in ovarian cancer patients was significantly correlated with age and CX3CL1 polymorphism factors; however, more in-depth effects and mechanisms need to be explored by large-scale, multicenter studies.
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Affiliation(s)
- Xin-Chen Wang
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen-Jing Jiang
- Department of Gynecological Oncology, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Peng Jiang
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei-Jian Ni
- Department of Pharmacy, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, the Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China,*Correspondence: Wei-Jian Ni,
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13
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Wang C, Zhou J, Wang L, Xing T, Dai H, Zhou Y, Qi L, Zhao Y, Huang C, Li D, Li H, Li MJ, Liu B, Zheng H, Chen K, Li L. ABO
blood groups and expression of blood group antigens of epithelial ovarian cancer in Chinese women. Cancer Med 2022; 12:7498-7507. [PMID: 36415180 PMCID: PMC10067109 DOI: 10.1002/cam4.5476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/07/2022] [Accepted: 11/13/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND ABO blood groups has been associated with risk of several cancers; however, the results for an association with ovarian cancer are inconsistent and little is known about the expression of histo-blood group (ABH) antigens and ABO gene in ovarian tumor tissues. METHODS To assess the impact of genotype-derived ABO blood types on the risk of EOC, we conducted a case-control study in 1,870 EOC and 4,829 controls. Expression of A and B antigen in 70 pairs of ovarian tumor tissues and adjacent normal tissues were detected by immunohistochemistry. Gene expression and DNA methylation profiling was conducted in ovarian tumor tissues. RESULTS We identified that blood group A was associated with increased risk for EOC compared to blood group O (OR = 1.18, 95% CI = 1.03-1.36, p = 0.019). Increased frequency of aberrant expression of histo-blood group antigens was observed in patients with blood group A (76.5%) compared to patients with blood group O (21.1%) and B (5.0%) by immunohistochemistry (p < 0.001). ABO gene expression was down-regulated in ovarian tumor tissues compared with paired adjacent normal tissues (p = 0.027). In addition, ABO gene expression was positively correlated with NFYB (r = 0.38, p < 0.001) and inversely correlated with DNA methylation level of four CpG sites on ABO gene (cg11879188, r = - 0.3, p = 0.002; cg22535403, r = - 0.30, p = 0.002; cg13506600, r = - 0.22, p = 0.025; cg07241568, r = - 0.21, p = 0.049) in ovarian tumor tissues. CONCLUSION We identified blood group A was associated with increased EOC risk in Chinese women and provided the clues of the possible molecular mechanisms of blood group A related to ovarian cancer risk.
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Affiliation(s)
- Chao Wang
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Jingjing Zhou
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Lili Wang
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Tongyu Xing
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Hongji Dai
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Yao Zhou
- Department of Pharmacology, the Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences Tianjin Medical University Tianjin China
| | - Lisha Qi
- Department of Pathology Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer Tianjin China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Caiyun Huang
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Ding Li
- Department of Clinical Laboratory Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer Tianjin P. R. China
| | - Haixin Li
- Cancer Biobank Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer Tianjin China
| | - Mulin Jun Li
- Department of Pharmacology, the Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences Tianjin Medical University Tianjin China
| | - Ben Liu
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
| | - Lian Li
- Department of Epidemiology and Biostatistics Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin Tianjin China
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Main C, Chen X, Zhao M, Chamley LW, Chen Q. Understanding How Pregnancy Protects Against Ovarian and Endometrial Cancer Development: Fetal Antigens May Be Involved. Endocrinology 2022; 163:6675223. [PMID: 36004540 PMCID: PMC9574549 DOI: 10.1210/endocr/bqac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Indexed: 11/19/2022]
Abstract
It is well known that many factors, including infertility, obesity, type 2 diabetes, and family history of cancer, increase the risk of developing endometrial and ovarian cancer. However, multiparous women are known to have a lower risk of developing either ovarian or endometrial cancer than nonparous women. The lack of ovulation and shifting of sex hormonal balance, with decreased estrogen levels and increased progesterone levels during pregnancy, has traditionally been thought to be the major contributor to this decreased risk. However, in reality, the mechanisms underlying this phenomenon are relatively unknown. Increasing evidence suggests that endocrine factors are unlikely to completely explain the protective effect of pregnancies, and that multiple other nonendocrine mechanisms including fetal antigens and the newly proposed dormant cells hypothesis may also be involved. In this review, we summarize recent evidence and describe the potential underlying mechanisms that may explain how pregnancy protects against the development of ovarian and endometrial cancers in women's later life.
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Affiliation(s)
- Claudia Main
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, The University of Auckland, Auckland 1141, New Zealand
| | - Xinyue Chen
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, The University of Auckland, Auckland 1141, New Zealand
| | - Min Zhao
- Department of Gynecological Cancer, Wuxi Maternity and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing 214002, China
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, The University of Auckland, Auckland 1141, New Zealand
| | - Qi Chen
- Correspondence: Qi Chen, MD, PhD, Department of Obstetrics and Gynaecology, Faculty of Medical and Health Science, The University of Auckland, Auckland, New Zealand. ; or Min Zhao, MD, PhD, Department of Gynecological Cancer, Wuxi Maternity and Child Health Hospital Affiliated to Nanjing Medical University, China.
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Genome-Wide Association Study of Fluorescent Oxidation Products Accounting for Tobacco Smoking Status in Adults from the French EGEA Study. Antioxidants (Basel) 2022; 11:antiox11050802. [PMID: 35624665 PMCID: PMC9137810 DOI: 10.3390/antiox11050802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress (OS) is the main pathophysiological mechanism involved in several chronic diseases, including asthma. Fluorescent oxidation products (FlOPs), a global biomarker of damage due to OS, is of growing interest in epidemiological studies. We conducted a genome-wide association study (GWAS) of the FlOPs level in 1216 adults from the case-control and family-based EGEA study (mean age 43 years old, 51% women, and 23% current smokers) to identify genetic variants associated with FlOPs. The GWAS was first conducted in the whole sample and then stratified according to smoking status, the main exogenous source of reactive oxygen species. Among the top genetic variants identified by the three GWAS, those located in BMP6 (p = 3 × 10−6), near BMPER (p = 9 × 10−6), in GABRG3 (p = 4 × 10−7), and near ATG5 (p = 2 × 10−9) are the most relevant because of both their link to biological pathways related to OS and their association with several chronic diseases for which the role of OS in their pathophysiology has been pointed out. BMP6 and BMPER are of particular interest due to their involvement in the same biological pathways related to OS and their functional interaction. To conclude, this study, which is the first GWAS of FlOPs, provides new insights into the pathophysiology of chronic OS-related diseases.
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16
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Dareng EO, Tyrer JP, Barnes DR, Jones MR, Yang X, Aben KKH, Adank MA, Agata S, Andrulis IL, Anton-Culver H, Antonenkova NN, Aravantinos G, Arun BK, Augustinsson A, Balmaña J, Bandera EV, Barkardottir RB, Barrowdale D, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bermisheva M, Bernardini MQ, Bjorge L, Black A, Bogdanova NV, Bonanni B, Borg A, Brenton JD, Budzilowska A, Butzow R, Buys SS, Cai H, Caligo MA, Campbell I, Cannioto R, Cassingham H, Chang-Claude J, Chanock SJ, Chen K, Chiew YE, Chung WK, Claes KBM, Colonna S, Cook LS, Couch FJ, Daly MB, Dao F, Davies E, de la Hoya M, de Putter R, Dennis J, DePersia A, Devilee P, Diez O, Ding YC, Doherty JA, Domchek SM, Dörk T, du Bois A, Dürst M, Eccles DM, Eliassen HA, Engel C, Evans GD, Fasching PA, Flanagan JM, Fortner RT, Machackova E, Friedman E, Ganz PA, Garber J, Gensini F, Giles GG, Glendon G, Godwin AK, Goodman MT, Greene MH, Gronwald J, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hansen TVO, Harris HR, Hartman M, Heitz F, Hildebrandt MAT, Høgdall E, Høgdall CK, Hopper JL, Huang RY, Huff C, Hulick PJ, Huntsman DG, Imyanitov EN, Isaacs C, Jakubowska A, James PA, Janavicius R, Jensen A, Johannsson OT, John EM, Jones ME, Kang D, Karlan BY, Karnezis A, Kelemen LE, Khusnutdinova E, Kiemeney LA, Kim BG, Kjaer SK, Komenaka I, Kupryjanczyk J, Kurian AW, Kwong A, Lambrechts D, Larson MC, Lazaro C, Le ND, Leslie G, Lester J, Lesueur F, Levine DA, Li L, Li J, Loud JT, Lu KH, Lubiński J, Mai PL, Manoukian S, Marks JR, Matsuno RK, Matsuo K, May T, McGuffog L, McLaughlin JR, McNeish IA, Mebirouk N, Menon U, Miller A, Milne RL, Minlikeeva A, Modugno F, Montagna M, Moysich KB, Munro E, Nathanson KL, Neuhausen SL, Nevanlinna H, Yie JNY, Nielsen HR, Nielsen FC, Nikitina-Zake L, Odunsi K, Offit K, Olah E, Olbrecht S, Olopade OI, Olson SH, Olsson H, Osorio A, Papi L, Park SK, Parsons MT, Pathak H, Pedersen IS, Peixoto A, Pejovic T, Perez-Segura P, Permuth JB, Peshkin B, Peterlongo P, Piskorz A, Prokofyeva D, Radice P, Rantala J, Riggan MJ, Risch HA, Rodriguez-Antona C, Ross E, Rossing MA, Runnebaum I, Sandler DP, Santamariña M, Soucy P, Schmutzler RK, Setiawan VW, Shan K, Sieh W, Simard J, Singer CF, Sokolenko AP, Song H, Southey MC, Steed H, Stoppa-Lyonnet D, Sutphen R, Swerdlow AJ, Tan YY, Teixeira MR, Teo SH, Terry KL, Terry MB, Thomassen M, Thompson PJ, Thomsen LCV, Thull DL, Tischkowitz M, Titus L, Toland AE, Torres D, Trabert B, Travis R, Tung N, Tworoger SS, Valen E, van Altena AM, van der Hout AH, Van Nieuwenhuysen E, van Rensburg EJ, Vega A, Edwards DV, Vierkant RA, Wang F, Wappenschmidt B, Webb PM, Weinberg CR, Weitzel JN, Wentzensen N, White E, Whittemore AS, Winham SJ, Wolk A, Woo YL, Wu AH, Yan L, Yannoukakos D, Zavaglia KM, Zheng W, Ziogas A, Zorn KK, Kleibl Z, Easton D, Lawrenson K, DeFazio A, Sellers TA, Ramus SJ, Pearce CL, Monteiro AN, Cunningham J, Goode EL, Schildkraut JM, Berchuck A, Chenevix-Trench G, Gayther SA, Antoniou AC, Pharoah PDP. Polygenic risk modeling for prediction of epithelial ovarian cancer risk. Eur J Hum Genet 2022; 30:349-362. [PMID: 35027648 PMCID: PMC8904525 DOI: 10.1038/s41431-021-00987-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 08/09/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
Polygenic risk scores (PRS) for epithelial ovarian cancer (EOC) have the potential to improve risk stratification. Joint estimation of Single Nucleotide Polymorphism (SNP) effects in models could improve predictive performance over standard approaches of PRS construction. Here, we implemented computationally efficient, penalized, logistic regression models (lasso, elastic net, stepwise) to individual level genotype data and a Bayesian framework with continuous shrinkage, "select and shrink for summary statistics" (S4), to summary level data for epithelial non-mucinous ovarian cancer risk prediction. We developed the models in a dataset consisting of 23,564 non-mucinous EOC cases and 40,138 controls participating in the Ovarian Cancer Association Consortium (OCAC) and validated the best models in three populations of different ancestries: prospective data from 198,101 women of European ancestries; 7,669 women of East Asian ancestries; 1,072 women of African ancestries, and in 18,915 BRCA1 and 12,337 BRCA2 pathogenic variant carriers of European ancestries. In the external validation data, the model with the strongest association for non-mucinous EOC risk derived from the OCAC model development data was the S4 model (27,240 SNPs) with odds ratios (OR) of 1.38 (95% CI: 1.28-1.48, AUC: 0.588) per unit standard deviation, in women of European ancestries; 1.14 (95% CI: 1.08-1.19, AUC: 0.538) in women of East Asian ancestries; 1.38 (95% CI: 1.21-1.58, AUC: 0.593) in women of African ancestries; hazard ratios of 1.36 (95% CI: 1.29-1.43, AUC: 0.592) in BRCA1 pathogenic variant carriers and 1.49 (95% CI: 1.35-1.64, AUC: 0.624) in BRCA2 pathogenic variant carriers. Incorporation of the S4 PRS in risk prediction models for ovarian cancer may have clinical utility in ovarian cancer prevention programs.
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Affiliation(s)
- Eileen O Dareng
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Jonathan P Tyrer
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Daniel R Barnes
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xin Yang
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Katja K H Aben
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
- Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands
| | - Muriel A Adank
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Family Cancer Clinic, Amsterdam, The Netherlands
| | - Simona Agata
- Veneto Institute of Oncology IOV-IRCCS, Immunology and Molecular Oncology Unit, Padua, Italy
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON, Canada
- University of Toronto, Department of Molecular Genetics, Toronto, ON, Canada
| | - Hoda Anton-Culver
- University of California Irvine, Department of Epidemiology, Genetic Epidemiology Research Institute, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | | | - Banu K Arun
- University of Texas MD Anderson Cancer Center, Department of Breast Medical Oncology, Houston, TX, USA
| | - Annelie Augustinsson
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Judith Balmaña
- Vall d'Hebron Institute of Oncology, Hereditary cancer Genetics Group, Barcelona, Spain
- University Hospital of Vall d'Hebron, Department of Medical Oncology, Barcelona, Spain
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, Cancer Prevention and Control Program, New Brunswick, NJ, USA
| | - Rosa B Barkardottir
- Landspitali University Hospital, Department of Pathology, Reykjavik, Iceland
- University of Iceland, BMC (Biomedical Centre), Faculty of Medicine, Reykjavik, Iceland
| | - Daniel Barrowdale
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Matthias W Beckmann
- University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - Alicia Beeghly-Fadiel
- Vanderbilt University School of Medicine, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Javier Benitez
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
- Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain
| | - Marina Bermisheva
- Ufa Federal Research Centre of the Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, Russia
| | - Marcus Q Bernardini
- Princess Margaret Hospital, Division of Gynecologic Oncology, University Health Network, Toronto, ON, Canada
| | - Line Bjorge
- Haukeland University Hospital, Department of Obstetrics and Gynecology, Bergen, Norway
- University of Bergen, Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Bergen, Norway
| | - Amanda Black
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Hannover Medical School, Department of Radiation Oncology, Hannover, Germany
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Bernardo Bonanni
- IEO, European Institute of Oncology IRCCS, Division of Cancer Prevention and Genetics, Milan, Italy
| | - Ake Borg
- Lund University and Skåne University Hospital, Department of Oncology, Lund, Sweden
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Agnieszka Budzilowska
- Maria Sklodowska-Curie National Research Institute of Oncology, Department of Pathology and Laboratory Diagnostics, Warsaw, Poland
| | - Ralf Butzow
- University of Helsinki, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - Saundra S Buys
- Huntsman Cancer Institute, Department of Medicine, Salt Lake City, UT, USA
| | - Hui Cai
- Vanderbilt University School of Medicine, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Maria A Caligo
- University Hospital, SOD Genetica Molecolare, Pisa, Italy
| | - Ian Campbell
- Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC, Australia
| | - Rikki Cannioto
- Roswell Park Cancer Institute, Cancer Pathology & Prevention, Division of Cancer Prevention and Population Sciences, Buffalo, NY, USA
| | - Hayley Cassingham
- Division of Human Genetics, The Ohio State University, Department of Internal Medicine, Columbus, OH, USA
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
- University Medical Center Hamburg-Eppendorf, Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany
| | - Stephen J Chanock
- National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Kexin Chen
- Tianjin Medical University Cancer Institute and Hospital, Department of Epidemiology, Tianjin, China
| | - Yoke-Eng Chiew
- The University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, NSW, Australia
| | - Wendy K Chung
- Columbia University, Departments of Pediatrics and Medicine, New York, NY, USA
| | | | - Sarah Colonna
- Huntsman Cancer Institute, Department of Medicine, Salt Lake City, UT, USA
| | - Linda S Cook
- University of New Mexico, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Alberta Health Services, Department of Cancer Epidemiology and Prevention Research, Calgary, AB, Canada
| | - Fergus J Couch
- Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, MN, USA
| | - Mary B Daly
- Fox Chase Cancer Center, Department of Clinical Genetics, Philadelphia, PA, USA
| | - Fanny Dao
- Memorial Sloan Kettering Cancer Center, Gynecology Service, Department of Surgery, New York, NY, USA
| | | | - Miguel de la Hoya
- CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Molecular Oncology Laboratory, Madrid, Spain
| | - Robin de Putter
- Ghent University, Centre for Medical Genetics, Gent, Belgium
| | - Joe Dennis
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Allison DePersia
- NorthShore University Health System, Center for Medical Genetics, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Peter Devilee
- Leiden University Medical Center, Department of Pathology, Leiden, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Orland Diez
- Vall dHebron Institute of Oncology (VHIO), Oncogenetics Group, Barcelona, Spain
- University Hospital Vall dHebron, Clinical and Molecular Genetics Area, Barcelona, Spain
| | - Yuan Chun Ding
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Jennifer A Doherty
- University of Utah, Huntsman Cancer Institute, Department of Population Health Sciences, Salt Lake City, UT, USA
| | - Susan M Domchek
- University of Pennsylvania, Basser Center for BRCA, Abramson Cancer Center, Philadelphia, PA, USA
| | - Thilo Dörk
- Hannover Medical School, Gynaecology Research Unit, Hannover, Germany
| | - Andreas du Bois
- Ev. Kliniken Essen-Mitte (KEM), Department of Gynecology and Gynecologic Oncology, Essen, Germany
- Dr. Horst Schmidt Kliniken Wiesbaden, Department of Gynecology and Gynecologic Oncology, Wiesbaden, Germany
| | - Matthias Dürst
- Jena University Hospital-Friedrich Schiller University, Department of Gynaecology, Jena, Germany
| | - Diana M Eccles
- University of Southampton, Faculty of Medicine, Southampton, UK
| | - Heather A Eliassen
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Brigham and Women's Hospital and Harvard Medical School, Channing Division of Network Medicine, Boston, MA, USA
| | - Christoph Engel
- University of Leipzig, Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
- University of Leipzig, LIFE-Leipzig Research Centre for Civilization Diseases, Leipzig, Germany
| | - Gareth D Evans
- University of Manchester, Manchester Academic Health Science Centre, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester, UK
- St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester, UK
| | - Peter A Fasching
- University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
- University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, Los Angeles, CA, USA
| | - James M Flanagan
- Imperial College London, Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, London, UK
| | - Renée T Fortner
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Eva Machackova
- Masaryk Memorial Cancer Institute, Department of Cancer Epidemiology and Genetics, Brno, Czech Republic
| | - Eitan Friedman
- Chaim Sheba Medical Center, The Susanne Levy Gertner Oncogenetics Unit, Ramat Gan, Israel
- Tel Aviv University, Sackler Faculty of Medicine, Ramat Aviv, Israel
| | - Patricia A Ganz
- Jonsson Comprehensive Cancer Centre, UCLA, Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Los Angeles, CA, USA
| | - Judy Garber
- Dana-Farber Cancer Institute, Cancer Risk and Prevention Clinic, Boston, MA, USA
| | - Francesca Gensini
- University of Florence, Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics Unit, Florence, Italy
| | - Graham G Giles
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, VIC, Australia
- The University of Melbourne, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, VIC, Australia
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC, Australia
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON, Canada
| | - Andrew K Godwin
- University of Kansas Medical Center, Department of Pathology and Laboratory Medicine, Kansas City, KS, USA
| | - Marc T Goodman
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Los Angeles, CA, USA
| | - Mark H Greene
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Jacek Gronwald
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
| | - Eric Hahnen
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology (CIO), Cologne, Germany
| | - Christopher A Haiman
- University of Southern California, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Niclas Håkansson
- Karolinska Institutet, Institute of Environmental Medicine, Stockholm, Sweden
| | - Ute Hamann
- German Cancer Research Center (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
| | - Thomas V O Hansen
- Rigshospitalet, Copenhagen University Hospital, Department of Clinical Genetics, Copenhagen, Denmark
| | - Holly R Harris
- Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, WA, USA
- University of Washington, Department of Epidemiology, Seattle, WA, USA
| | - Mikael Hartman
- National University of Singapore and National University Health System, Saw Swee Hock School of Public Health, Singapore, Singapore
- National University Health System, Department of Surgery, Singapore, Singapore
| | - Florian Heitz
- Ev. Kliniken Essen-Mitte (KEM), Department of Gynecology and Gynecologic Oncology, Essen, Germany
- Dr. Horst Schmidt Kliniken Wiesbaden, Department of Gynecology and Gynecologic Oncology, Wiesbaden, Germany
- Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Berlin, Germany
| | | | - Estrid Høgdall
- Danish Cancer Society Research Center, Department of Virus, Lifestyle and Genes, Copenhagen, Denmark
- University of Copenhagen, Molecular Unit, Department of Pathology, Herlev Hospital, Copenhagen, Denmark
| | - Claus K Høgdall
- University of Copenhagen, Department of Gynaecology, Rigshospitalet, Copenhagen, Denmark
| | - John L Hopper
- The University of Melbourne, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, VIC, Australia
| | - Ruea-Yea Huang
- Roswell Park Cancer Institute, Center For Immunotherapy, Buffalo, NY, USA
| | - Chad Huff
- University of Texas MD Anderson Cancer Center, Department of Epidemiology, Houston, TX, USA
| | - Peter J Hulick
- NorthShore University Health System, Center for Medical Genetics, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - David G Huntsman
- BC Cancer, Vancouver General Hospital, and University of British Columbia, British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver, BC, Canada
- University of British Columbia, Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
- University of British Columbia, Department of Obstetrics and Gynecology, Vancouver, BC, Canada
- BC Cancer Research Centre, Department of Molecular Oncology, Vancouver, BC, Canada
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Anna Jakubowska
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
- Pomeranian Medical University, Independent Laboratory of Molecular Biology and Genetic Diagnostics, Szczecin, Poland
| | - Paul A James
- The University of Melbourne, Sir Peter MacCallum Department of Oncology, Melbourne, VIC, Australia
- Peter MacCallum Cancer Center, Parkville Familial Cancer Centre, Melbourne, VIC, Australia
| | - Ramunas Janavicius
- Vilnius University Hospital Santariskiu Clinics, Hematology, oncology and transfusion medicine center, Dept. of Molecular and Regenerative Medicine, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Allan Jensen
- Danish Cancer Society Research Center, Department of Virus, Lifestyle and Genes, Copenhagen, Denmark
| | | | - Esther M John
- Stanford University School of Medicine, Department of Epidemiology & Population Health, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA, USA
| | - Michael E Jones
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
| | - Daehee Kang
- Seoul National University College of Medicine, Department of Preventive Medicine, Seoul, Korea
- Seoul National University Graduate School, Department of Biomedical Sciences, Seoul, Korea
- Seoul National University, Cancer Research Institute, Seoul, Korea
| | - Beth Y Karlan
- University of California at Los Angeles, David Geffen School of Medicine, Department of Obstetrics and Gynecology, Los Angeles, CA, USA
| | - Anthony Karnezis
- UC Davis Medical Center, Department of Pathology and Laboratory Medicine, Sacramento, CA, USA
| | - Linda E Kelemen
- Medical University of South Carolina, Hollings Cancer Center, Charleston, SC, USA
| | - Elza Khusnutdinova
- Ufa Federal Research Centre of the Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, Russia
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Byoung-Gie Kim
- Sungkyunkwan University School of Medicine, Department of Obstetrics and Gynecology, Samsung Medical Center, Seoul, Korea
| | - Susanne K Kjaer
- Danish Cancer Society Research Center, Department of Virus, Lifestyle and Genes, Copenhagen, Denmark
- University of Copenhagen, Department of Gynaecology, Rigshospitalet, Copenhagen, Denmark
| | - Ian Komenaka
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Jolanta Kupryjanczyk
- Maria Sklodowska-Curie National Research Institute of Oncology, Department of Pathology and Laboratory Diagnostics, Warsaw, Poland
| | - Allison W Kurian
- Stanford University School of Medicine, Department of Epidemiology & Population Health, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Department of Medicine, Division of Oncology, Stanford, CA, USA
| | - Ava Kwong
- Cancer Genetics Centre, Hong Kong Hereditary Breast Cancer Family Registry, Happy Valley, Hong Kong
- The University of Hong Kong, Department of Surgery, Pok Fu Lam, Hong Kong
- Hong Kong Sanatorium and Hospital, Department of Surgery, Happy Valley, Hong Kong
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- University of Leuven, Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium
| | - Melissa C Larson
- Mayo Clinic, Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Rochester, MN, USA
| | - Conxi Lazaro
- ONCOBELL-IDIBELL-IGTP, Catalan Institute of Oncology, CIBERONC, Hereditary Cancer Program, Barcelona, Spain
| | - Nhu D Le
- BC Cancer, Cancer Control Research, Vancouver, BC, Canada
| | - Goska Leslie
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Jenny Lester
- University of California at Los Angeles, David Geffen School of Medicine, Department of Obstetrics and Gynecology, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- Inserm U900, Genetic Epidemiology of Cancer team, Paris, France
| | - Douglas A Levine
- Memorial Sloan Kettering Cancer Center, Gynecology Service, Department of Surgery, New York, NY, USA
- NYU Langone Medical Center, Gynecologic Oncology, Laura and Isaac Pearlmutter Cancer Center, New York, NY, USA
| | - Lian Li
- Tianjin Medical University Cancer Institute and Hospital, Department of Epidemiology, Tianjin, China
| | - Jingmei Li
- Genome Institute of Singapore, Human Genetics Division, Singapore, Singapore
| | - Jennifer T Loud
- National Cancer Institute, Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Karen H Lu
- University of Texas MD Anderson Cancer Center, Department of Gynecologic Oncology and Clinical Cancer Genetics Program, Houston, TX, USA
| | - Jan Lubiński
- Pomeranian Medical University, Department of Genetics and Pathology, Szczecin, Poland
| | - Phuong L Mai
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Siranoush Manoukian
- Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Unit of Medical Genetics, Department of Medical Oncology and Hematology, Milan, Italy
| | - Jeffrey R Marks
- Duke University Hospital, Department of Surgery, Durham, NC, USA
| | - Rayna Kim Matsuno
- University of Hawaii Cancer Center, Cancer Epidemiology Program, Honolulu, HI, USA
| | - Keitaro Matsuo
- Aichi Cancer Center Research Institute, Division of Cancer Epidemiology and Prevention, Nagoya, Japan
- Nagoya University Graduate School of Medicine, Division of Cancer Epidemiology, Nagoya, Japan
| | - Taymaa May
- Princess Margaret Hospital, Division of Gynecologic Oncology, University Health Network, Toronto, ON, Canada
| | - Lesley McGuffog
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - John R McLaughlin
- Samuel Lunenfeld Research Institute, Public Health Ontario, Toronto, ON, Canada
| | - Iain A McNeish
- Imperial College London, Division of Cancer and Ovarian Cancer Action Research Centre, Department Surgery & Cancer, London, UK
- University of Glasgow, Institute of Cancer Sciences, Glasgow, UK
| | - Noura Mebirouk
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- Inserm U900, Genetic Epidemiology of Cancer team, Paris, France
| | - Usha Menon
- University College London, MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Austin Miller
- Roswell Park Cancer Institute, NRG Oncology, Statistics and Data Management Center, Buffalo, NY, USA
| | - Roger L Milne
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, VIC, Australia
- The University of Melbourne, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Melbourne, VIC, Australia
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC, Australia
| | - Albina Minlikeeva
- Roswell Park Cancer Institute, Division of Cancer Prevention and Control, Buffalo, NY, USA
| | - Francesmary Modugno
- Magee-Womens Research Institute and Hillman Cancer Center, Womens Cancer Research Center, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA
| | - Marco Montagna
- Veneto Institute of Oncology IOV-IRCCS, Immunology and Molecular Oncology Unit, Padua, Italy
| | - Kirsten B Moysich
- Roswell Park Cancer Institute, Division of Cancer Prevention and Control, Buffalo, NY, USA
| | - Elizabeth Munro
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR, USA
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA
| | - Katherine L Nathanson
- University of Pennsylvania, Basser Center for BRCA, Abramson Cancer Center, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Heli Nevanlinna
- University of Helsinki, Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Joanne Ngeow Yuen Yie
- National Cancer Centre, Cancer Genetics Service, Singapore, Singapore
- Nanyang Technological University, Lee Kong Chian School of Medicine, Singapore, Singapore
| | | | - Finn C Nielsen
- Rigshospitalet, Copenhagen University Hospital, Department of Clinical Genetics, Copenhagen, Denmark
| | | | - Kunle Odunsi
- Roswell Park Cancer Institute, Department of Gynecologic Oncology, Buffalo, NY, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, Clinical Genetics Service, Department of Medicine, New York, NY, USA
| | - Edith Olah
- National Institute of Oncology, Department of Molecular Genetics, Budapest, Hungary
| | - Siel Olbrecht
- University Hospitals Leuven, Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, Leuven, Belgium
| | | | - Sara H Olson
- Memorial Sloan-Kettering Cancer Center, Department of Epidemiology and Biostatistics, New York, NY, USA
| | - Håkan Olsson
- Lund University, Department of Cancer Epidemiology, Clinical Sciences, Lund, Sweden
| | - Ana Osorio
- Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Laura Papi
- University of Florence, Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', Medical Genetics Unit, Florence, Italy
| | - Sue K Park
- Seoul National University College of Medicine, Department of Preventive Medicine, Seoul, Korea
- Seoul National University Graduate School, Department of Biomedical Sciences, Seoul, Korea
- Seoul National University, Cancer Research Institute, Seoul, Korea
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD, Australia
| | - Harsha Pathak
- University of Kansas Medical Center, Department of Pathology and Laboratory Medicine, Kansas City, KS, USA
| | - Inge Sokilde Pedersen
- Aalborg University Hospital, Molecular Diagnostics, Aalborg, Denmark
- Aalborg University Hospital, Clinical Cancer Research Center, Aalborg, Denmark
- Aalborg University, Department of Clinical Medicine, Aalborg, Denmark
| | - Ana Peixoto
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
| | - Tanja Pejovic
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR, USA
- Oregon Health & Science University, Knight Cancer Institute, Portland, OR, USA
| | - Pedro Perez-Segura
- CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Molecular Oncology Laboratory, Madrid, Spain
| | - Jennifer B Permuth
- Moffitt Cancer Center, Department of Cancer Epidemiology, Tampa, FL, USA
| | - Beth Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- IFOM-the FIRC Institute of Molecular Oncology, Genome Diagnostics Program, Milan, Italy
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Darya Prokofyeva
- Bashkir State University, Department of Genetics and Fundamental Medicine, Ufa, Russia
| | - Paolo Radice
- Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Milan, Italy
| | | | - Marjorie J Riggan
- Duke University Hospital, Department of Gynecologic Oncology, Durham, NC, USA
| | - Harvey A Risch
- Yale School of Public Health, Chronic Disease Epidemiology, New Haven, CT, USA
| | - Cristina Rodriguez-Antona
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
- Spanish National Cancer Research Centre (CNIO), Human Cancer Genetics Programme, Madrid, Spain
| | - Eric Ross
- Fox Chase Cancer Center, Population Studies Facility, Philadelphia, PA, USA
| | - Mary Anne Rossing
- Fred Hutchinson Cancer Research Center, Program in Epidemiology, Division of Public Health Sciences, Seattle, WA, USA
- University of Washington, Department of Epidemiology, Seattle, WA, USA
| | - Ingo Runnebaum
- Jena University Hospital-Friedrich Schiller University, Department of Gynaecology, Jena, Germany
| | - Dale P Sandler
- National Institute of Environmental Health Sciences, NIH, Epidemiology Branch, Research Triangle Park, NC, USA
| | - Marta Santamariña
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega Medicina Xenómica, Santiago De Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, Santiago De Compostela, Spain
| | - Penny Soucy
- Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Genomics Center, Québec City, QC, Canada
| | - Rita K Schmutzler
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology (CIO), Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - V Wendy Setiawan
- University of Southern California, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Kang Shan
- Hebei Medical University, Fourth Hospital, Department of Obstetrics and Gynaecology, Shijiazhuang, China
| | - Weiva Sieh
- Icahn School of Medicine at Mount Sinai, Department of Population Health Science and Policy, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York, NY, USA
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Genomic Center, Québec City, QC, Canada
| | - Christian F Singer
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
| | | | - Honglin Song
- University of Cambridge, Department of Public Health and Primary Care, Cambridge, UK
| | - Melissa C Southey
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, VIC, Australia
- Monash University, Precision Medicine, School of Clinical Sciences at Monash Health, Clayton, VIC, Australia
- The University of Melbourne, Department of Clinical Pathology, Melbourne, VIC, Australia
| | - Helen Steed
- Royal Alexandra Hospital, Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Edmonton, AB, Canada
| | - Dominique Stoppa-Lyonnet
- INSERM U830, Department of Tumour Biology, Paris, France
- Institut Curie, Service de Génétique, Paris, France
- Université Paris Descartes, Paris, France
| | - Rebecca Sutphen
- University of South Florida, Epidemiology Center, College of Medicine, Tampa, FL, USA
| | - Anthony J Swerdlow
- The Institute of Cancer Research, Division of Genetics and Epidemiology, London, UK
- The Institute of Cancer Research, Division of Breast Cancer Research, London, UK
| | - Yen Yen Tan
- Medical University of Vienna, Dept of OB/GYN and Comprehensive Cancer Center, Vienna, Austria
| | - Manuel R Teixeira
- Portuguese Oncology Institute, Department of Genetics, Porto, Portugal
- University of Porto, Biomedical Sciences Institute (ICBAS), Porto, Portugal
| | - Soo Hwang Teo
- Cancer Research Malaysia, Breast Cancer Research Programme, Subang Jaya, Selangor, Malaysia
- University of Malaya, Department of Surgery, Faculty of Medicine, Kuala Lumpur, Malaysia
| | - Kathryn L Terry
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Brigham and Women's Hospital and Harvard Medical School, Obstetrics and Gynecology Epidemiology Center, Boston, MA, USA
| | - Mary Beth Terry
- Columbia University, Department of Epidemiology, Mailman School of Public Health, New York, NY, USA
| | - Mads Thomassen
- Odense University Hospital, Department of Clinical Genetics, Odence C, Denmark
| | - Pamela J Thompson
- Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Los Angeles, CA, USA
| | - Liv Cecilie Vestrheim Thomsen
- Haukeland University Hospital, Department of Obstetrics and Gynecology, Bergen, Norway
- University of Bergen, Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Bergen, Norway
| | - Darcy L Thull
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Department of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- McGill University, Program in Cancer Genetics, Departments of Human Genetics and Oncology, Montréal, QC, Canada
- University of Cambridge, Department of Medical Genetics, Cambridge, UK
| | - Linda Titus
- Dartmouth College, Geisel School of Medicine, Hanover, NH, USA
| | - Amanda E Toland
- The Ohio State University, Department of Cancer Biology and Genetics, Columbus, OH, USA
| | - Diana Torres
- German Cancer Research Center (DKFZ), Molecular Genetics of Breast Cancer, Heidelberg, Germany
- Pontificia Universidad Javeriana, Institute of Human Genetics, Bogota, Colombia
| | - Britton Trabert
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Ruth Travis
- University of Oxford, Cancer Epidemiology Unit, Oxford, UK
| | - Nadine Tung
- Beth Israel Deaconess Medical Center, Department of Medical Oncology, Boston, MA, USA
| | - Shelley S Tworoger
- Harvard T.H. Chan School of Public Health, Department of Epidemiology, Boston, MA, USA
- Moffitt Cancer Center, Department of Cancer Epidemiology, Tampa, FL, USA
| | - Ellen Valen
- Haukeland University Hospital, Department of Obstetrics and Gynecology, Bergen, Norway
- University of Bergen, Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, Bergen, Norway
| | - Anne M van Altena
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Annemieke H van der Hout
- University Medical Center Groningen, University Groningen, Department of Genetics, Groningen, The Netherlands
| | - Els Van Nieuwenhuysen
- University Hospitals Leuven, Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, Leuven, Belgium
| | | | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Digna Velez Edwards
- Vanderbilt University Medical Center, Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Women's Health Research, Nashville, TN, USA
| | - Robert A Vierkant
- Mayo Clinic, Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Rochester, MN, USA
| | - Frances Wang
- Duke Cancer Institute, Cancer Control and Population Sciences, Durham, NC, USA
- Duke University Hospital, Department of Community and Family Medicine, Durham, NC, USA
| | - Barbara Wappenschmidt
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Familial Breast and Ovarian Cancer, Cologne, Germany
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Center for Integrated Oncology (CIO), Cologne, Germany
| | - Penelope M Webb
- QIMR Berghofer Medical Research Institute, Population Health Department, Brisbane, QLD, Australia
| | - Clarice R Weinberg
- National Institute of Environmental Health Sciences, NIH, Biostatistics and Computational Biology Branch, Research Triangle Park, NC, USA
| | | | - Nicolas Wentzensen
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Bethesda, MD, USA
| | - Emily White
- University of Washington, Department of Epidemiology, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alice S Whittemore
- Stanford University School of Medicine, Department of Epidemiology & Population Health, Stanford, CA, USA
- Stanford University School of Medicine, Department of Biomedical Data Science, Stanford, CA, USA
| | - Stacey J Winham
- Mayo Clinic, Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Rochester, MN, USA
| | - Alicja Wolk
- Karolinska Institutet, Institute of Environmental Medicine, Stockholm, Sweden
- Uppsala University, Department of Surgical Sciences, Uppsala, Sweden
| | - Yin-Ling Woo
- University of Malaya, Department of Obstetrics and Gynaecology, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Anna H Wu
- University of Southern California, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Li Yan
- Hebei Medical University, Fourth Hospital, Department of Molecular Biology, Shijiazhuang, China
| | - Drakoulis Yannoukakos
- National Centre for Scientific Research 'Demokritos', Molecular Diagnostics Laboratory, INRASTES, Athens, Greece
| | | | - Wei Zheng
- Vanderbilt University School of Medicine, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Argyrios Ziogas
- University of California Irvine, Department of Epidemiology, Genetic Epidemiology Research Institute, Irvine, CA, USA
| | - Kristin K Zorn
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty od Medicine, Charles University, Prague, Czech Republic
| | - Douglas Easton
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Centre, Department of Obstetrics and Gynecology, Los Angeles, CA, USA
| | - Anna DeFazio
- The University of Sydney, Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- Westmead Hospital, Department of Gynaecological Oncology, Sydney, NSW, Australia
| | | | - Susan J Ramus
- University of NSW Sydney, School of Women's and Children's Health, Faculty of Medicine, Sydney, NSW, Australia
- University of NSW Sydney, Adult Cancer Program, Lowy Cancer Research Centre, Sydney, NSW, Australia
| | - Celeste L Pearce
- University of Michigan School of Public Health, Department of Epidemiology, Ann Arbor, MI, USA
- University of Southern California Norris Comprehensive Cancer Center, Department of Preventive Medicine, Keck School of Medicine, Los Angeles, CA, USA
| | - Alvaro N Monteiro
- Moffitt Cancer Center, Department of Cancer Epidemiology, Tampa, FL, USA
| | - Julie Cunningham
- Mayo Clinic, Department of Health Science Research, Division of Epidemiology, Rochester, MN, USA
| | - Ellen L Goode
- Mayo Clinic, Department of Health Science Research, Division of Epidemiology, Rochester, MN, USA
| | - Joellen M Schildkraut
- Emory University, Department of Epidemiology, Rollins School of Public Health, Atlanta, GA, USA
| | - Andrew Berchuck
- Duke University Hospital, Department of Gynecologic Oncology, Durham, NC, USA
| | - Georgia Chenevix-Trench
- QIMR Berghofer Medical Research Institute, Department of Genetics and Computational Biology, Brisbane, QLD, Australia
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Antonis C Antoniou
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK
| | - Paul D P Pharoah
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Cambridge, UK.
- University of Cambridge, Centre for Cancer Genetic Epidemiology, Department of Oncology, Cambridge, UK.
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17
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Dai H, Chu X, Liang Q, Wang M, Li L, Zhou Y, Zheng Z, Wang W, Wang Z, Li H, Wang J, Zheng H, Zhao Y, Liu L, Yao H, Luo M, Wang Q, Kang S, Li Y, Wang K, Song F, Zhang R, Wu X, Cheng X, Zhang W, Wei Q, Li MJ, Chen K. Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. Cell Discov 2021; 7:121. [PMID: 34930913 PMCID: PMC8688503 DOI: 10.1038/s41421-021-00342-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Ovarian cancer survival varies considerably among patients, to which germline variation may also contribute in addition to mutational signatures. To identify genetic markers modulating ovarian cancer outcome, we performed a genome-wide association study in 2130 Chinese ovarian cancer patients and found a hitherto unrecognized locus at 3p26.1 to be associated with the overall survival (Pcombined = 8.90 × 10−10). Subsequent statistical fine-mapping, functional annotation, and eQTL mapping prioritized a likely casual SNP rs9311399 in the non-coding regulatory region. Mechanistically, rs9311399 altered its enhancer activity through an allele-specific transcription factor binding and a long-range interaction with the promoter of a lncRNA BHLHE40-AS1. Deletion of the rs9311399-associated enhancer resulted in expression changes in several oncogenic signaling pathway genes and a decrease in tumor growth. Thus, we have identified a novel genetic locus that is associated with ovarian cancer survival possibly through a long-range gene regulation of oncogenic pathways.
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Affiliation(s)
- Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yao Zhou
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhanye Zheng
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Zhao Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Haixin Li
- Cancer Biobank, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Luyang Liu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Menghan Luo
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qiong Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shan Kang
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Ke Wang
- Department of Gynecologic Oncology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoxin Zhang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Cheng
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China. .,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China. .,Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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18
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Bukina ES, Kondratyev NV, Kozin SV, Golimbet VE, Artyuhov AS, Dashinimaev EB. SLC6A1 and Neuropsychiatric Diseases: The Role of Mutations and Prospects for Treatment with Genome Editing Systems. NEUROCHEM J+ 2021. [DOI: 10.1134/s1819712421040048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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ETV5-mediated upregulation of lncRNA CTBP1-DT as a ceRNA facilitates HGSOC progression by regulating miR-188-5p/MAP3K3 axis. Cell Death Dis 2021; 12:1146. [PMID: 34887384 PMCID: PMC8660778 DOI: 10.1038/s41419-021-04256-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is a common and lethal cancer of the female reproductive system. Long non-coding RNAs (lncRNAs) are aberrantly expressed in various cancers and play crucial roles in tumour progression. However, their function and molecular mechanism in HGSOC remain largely unknown. Based on public databases and bioinformatics analyses, the overexpression of lncRNA CTBP1-DT in HGSOC tissues was detected and validated in a cohort of HGSOC tissues. High expression of lncRNA CTBP1-DT was associated with poor prognosis and was an independent risk factor for survival. Overexpression of lncRNA CTBP1-DT promoted malignant biological behaviour of HGSOC cells, whereas its depletion induced growth arrest of HGSOC cells by vitro and in vivo assays. Mechanistically, lncRNA CTBP1-DT could competitively bind to miR-188-5p to protect MAP3K3 from degradation. Moreover, our results revealed that ETV5 could specifically interact with the promoter of lncRNA CTBP1-DT and activate its transcription. Collectively, these results reveal a novel ETV5/lncRNA CTBP1-DT/miR-188-5p/MAP3K3 pathway for HGSOC progression and suggest that lncRNA CTBP1-DT might be a potential biomarker and therapeutic target for HGSOC. ![]()
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20
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Kar SP, Considine DP, Tyrer JP, Plummer JT, Chen S, Dezem FS, Barbeira AN, Rajagopal PS, Rosenow WT, Moreno F, Bodelon C, Chang-Claude J, Chenevix-Trench G, deFazio A, Dörk T, Ekici AB, Ewing A, Fountzilas G, Goode EL, Hartman M, Heitz F, Hillemanns P, Høgdall E, Høgdall CK, Huzarski T, Jensen A, Karlan BY, Khusnutdinova E, Kiemeney LA, Kjaer SK, Klapdor R, Köbel M, Li J, Liebrich C, May T, Olsson H, Permuth JB, Peterlongo P, Radice P, Ramus SJ, Riggan MJ, Risch HA, Saloustros E, Simard J, Szafron LM, Titus L, Thompson CL, Vierkant RA, Winham SJ, Zheng W, Doherty JA, Berchuck A, Lawrenson K, Im HK, Manichaikul AW, Pharoah PD, Gayther SA, Schildkraut JM. Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies candidate susceptibility genes for breast and ovarian cancer. HGG ADVANCES 2021; 2:100042. [PMID: 34317694 PMCID: PMC8312632 DOI: 10.1016/j.xhgg.2021.100042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Familial, sequencing, and genome-wide association studies (GWASs) and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWASs) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through application of a pleiotropy-guided conditional/conjunction false discovery rate (FDR) approach in the setting of a TWASs. This identified 14 candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were >1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. The 22 genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.
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Affiliation(s)
- Siddhartha P. Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniel P.C. Considine
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jasmine T. Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe S. Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Padma S. Rajagopal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Will T. Rosenow
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Moreno
- Department of Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen, Erlangen, Germany
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang., Essen, Germany
- Department of Gynecology, Center for Oncologic Surgery, Charité Campus Virchow-Klinikum, Berlin, Germany
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - 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 K. Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Department of Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Allan Jensen
- Department of Lifestyle, Reproduction, and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Lambertus A. Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - 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
| | - Rüdiger Klapdor
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Foothills Medical Center, Calgary, AB, Canada
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore
| | - Clemens Liebrich
- Department of Obstetrics and Gynecology, Klinikum Wolfsburg, Wolfsburg, Germany
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Håkan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jennifer B. Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Marjorie J. Riggan
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | | | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Lukasz M. Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Linda Titus
- Muskie School of Public Service, University of Southern Maine, Portland, ME, USA
| | - Cheryl L. Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A. Vierkant
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joellen M. Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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21
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Considine DPC, Jia G, Shu X, Schildkraut JM, Pharoah PDP, Zheng W, Kar SP. Genetically predicted circulating protein biomarkers and ovarian cancer risk. Gynecol Oncol 2021; 160:506-513. [PMID: 33246661 PMCID: PMC7855757 DOI: 10.1016/j.ygyno.2020.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/15/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Most women with epithelial ovarian cancer (EOC) are diagnosed after the disease has metastasized and survival in this group remains poor. Circulating proteins associated with the risk of developing EOC have the potential to serve as biomarkers for early detection and diagnosis. We integrated large-scale genomic and proteomic data to identify novel plasma proteins associated with EOC risk. METHODS We used the germline genetic variants most strongly associated (P <1.5 × 10-11) with plasma levels of 1329 proteins in 3301 healthy individuals from the INTERVAL study to predict circulating levels of these proteins in 22,406 EOC cases and 40,941 controls from the Ovarian Cancer Association Consortium (OCAC). Association testing was performed by weighting the beta coefficients and standard errors for EOC risk from the OCAC study by the inverse of the beta coefficients from INTERVAL. RESULTS We identified 26 proteins whose genetically predicted circulating levels were associated with EOC risk at false discovery rate < 0.05. The 26 proteins included MFAP2, SEMG2, DLK1, and NTNG1 and a group of 22 proteins whose plasma levels were predicted by variants at chromosome 9q34.2. All 26 protein association signals identified were driven by association with the high-grade serous histotype that comprised 58% of the EOC cases in OCAC. Regional genomic plots confirmed overlap of the genetic association signal underlying both plasma protein level and EOC risk for the 26 proteins. Pathway analysis identified enrichment of seven biological pathways among the 26 proteins (Padjusted <0.05), highlighting roles for Focal Adhesion-PI3K-Akt-mTOR and Notch signaling. CONCLUSION The identified proteins further illuminate the etiology of EOC and represent promising new EOC biomarkers for targeted validation by studies involving direct measurement of plasma proteins in EOC patient cohorts.
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Affiliation(s)
- Daniel P C Considine
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Guochong Jia
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiang Shu
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joellen M Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siddhartha P Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
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22
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Fritsche LG, Patil S, Beesley LJ, VandeHaar P, Salvatore M, Ma Y, Peng RB, Taliun D, Zhou X, Mukherjee B. Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. Am J Hum Genet 2020; 107:815-836. [PMID: 32991828 PMCID: PMC7675001 DOI: 10.1016/j.ajhg.2020.08.025] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
To facilitate scientific collaboration on polygenic risk scores (PRSs) research, we created an extensive PRS online repository for 35 common cancer traits integrating freely available genome-wide association studies (GWASs) summary statistics from three sources: published GWASs, the NHGRI-EBI GWAS Catalog, and UK Biobank-based GWASs. Our framework condenses these summary statistics into PRSs using various approaches such as linkage disequilibrium pruning/p value thresholding (fixed or data-adaptively optimized thresholds) and penalized, genome-wide effect size weighting. We evaluated the PRSs in two biobanks: the Michigan Genomics Initiative (MGI), a longitudinal biorepository effort at Michigan Medicine, and the population-based UK Biobank (UKB). For each PRS construct, we provide measures on predictive performance and discrimination. Besides PRS evaluation, the Cancer-PRSweb platform features construct downloads and phenome-wide PRS association study results (PRS-PheWAS) for predictive PRSs. We expect this integrated platform to accelerate PRS-related cancer research.
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Affiliation(s)
- Lars G Fritsche
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Snehal Patil
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Lauren J Beesley
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Peter VandeHaar
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Maxwell Salvatore
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Ying Ma
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Robert B Peng
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Statistics, Northwestern University, Evanston, IL 60208, USA
| | - Daniel Taliun
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Bhramar Mukherjee
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Precision Health Data Science, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
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23
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Yan Z, Gu YY, Hu XD, Zhao Q, Kang HL, Wang M, Duan W, Guan Y. Clinical outcomes and safety of apatinib monotherapy in the treatment of patients with advanced epithelial ovarian carcinoma who progressed after standard regimens and the analysis of the VEGFR2 polymorphism. Oncol Lett 2020; 20:3035-3045. [PMID: 32782621 DOI: 10.3892/ol.2020.11857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/05/2020] [Indexed: 12/30/2022] Open
Abstract
The aims of the present study were to investigate the clinical outcomes and safety of apatinib monotherapy in the treatment of patients with advanced epithelial ovarian carcinoma (EOC) who have progressed after standard regimens, and to analyze the vascular endothelial growth factor receptor 2 (VEGFR2) rs2071559 polymorphism. A total of 118 patients with advanced EOC who received apatinib treatment were included in the study. Tumor response was evaluated using progression-free survival (PFS) and overall survival (OS) time, and safety data were documented. Additionally, peripheral blood and peripheral blood mononuclear cell (PBMC) specimens from the patients with EOC were collected to perform the genotyping of genetic polymorphism and assess the mRNA expression of VEGFR2, respectively. The objective response rate across the 118 patients with advanced EOC was 38.98%, the disease control rate was 63.56%, the median PFS time was 4.65 months and the median OS time was 15.10 months. Regarding the polymorphism analysis, the prevalence of rs2071559 in VEGFR2 among the 118 patients with advanced EOC was recorded as the TT genotype in 72 cases (61.02%), TC genotype in 41 cases (34.75%) and CC genotype in 5 cases (4.23%), and the minor allele frequency of rs2071559 was 0.22. The distribution of the three genotypes was in accordance with the Hardy-Weinberg equilibrium (P=0.781). TC and CC genotypes were merged in the subsequent analysis. The prognosis analyses suggested that the median PFS time of patients with the TC/CC genotype and the TT genotype was 3.10 and 5.40 months, respectively (P=0.015). Moreover, the median OS time of the two genotypes was 12.60 and 17.50 months, respectively (P=0.009). However, no association was noted between genotype status of the polymorphism and adverse reactions. Additionally, the mRNA expression analysis indicated that the mRNA expression levels of VEGFR2 in PBMC specimens were significantly different between TT and TC/CC genotypes (P<0.001). The present study suggested that the clinical outcomes of patients with advanced EOC, who progressed after standard regimens and received apatinib treatment, might be influenced by the VEGFR2 rs2071559 polymorphism.
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Affiliation(s)
- Zhen Yan
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Yuan-Yuan Gu
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Xiao-Di Hu
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Qun Zhao
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Hai-Li Kang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Miao Wang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Wei Duan
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, P.R. China
| | - Yin Guan
- Department of Oncology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
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24
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Manichaikul A, Peres LC, Wang XQ, Barnard ME, Chyn D, Sheng X, Du Z, Tyrer J, Dennis J, Schwartz AG, Cote ML, Peters E, Moorman PG, Bondy M, Barnholtz-Sloan JS, Terry P, Alberg AJ, Bandera EV, Funkhouser E, Wu AH, Pearce CL, Pike M, Setiawan VW, Haiman CA, Palmer JR, LeMarchand L, Wilkens LR, Berchuck A, Doherty JA, Modugno F, Ness R, Moysich K, Karlan BY, Whittemore AS, McGuire V, Sieh W, Lawrenson K, Gayther S, Sellers TA, Pharoah P, Schildkraut JM. Identification of novel epithelial ovarian cancer loci in women of African ancestry. Int J Cancer 2020; 146:2987-2998. [PMID: 31469419 PMCID: PMC7523187 DOI: 10.1002/ijc.32653] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/29/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022]
Abstract
Women of African ancestry have lower incidence of epithelial ovarian cancer (EOC) yet worse survival compared to women of European ancestry. We conducted a genome-wide association study in African ancestry women with 755 EOC cases, including 537 high-grade serous ovarian carcinomas (HGSOC) and 1,235 controls. We identified four novel loci with suggestive evidence of association with EOC (p < 1 × 10-6 ), including rs4525119 (intronic to AKR1C3), rs7643459 (intronic to LOC101927394), rs4286604 (12 kb 3' of UGT2A2) and rs142091544 (5 kb 5' of WWC1). For HGSOC, we identified six loci with suggestive evidence of association including rs37792 (132 kb 5' of follistatin [FST]), rs57403204 (81 kb 3' of MAGEC1), rs79079890 (LOC105376360 intronic), rs66459581 (5 kb 5' of PRPSAP1), rs116046250 (GABRG3 intronic) and rs192876988 (32 kb 3' of GK2). Among the identified variants, two are near genes known to regulate hormones and diseases of the ovary (AKR1C3 and FST), and two are linked to cancer (AKR1C3 and MAGEC1). In follow-up studies of the 10 identified variants, the GK2 region SNP, rs192876988, showed an inverse association with EOC in European ancestry women (p = 0.002), increased risk of ER positive breast cancer in African ancestry women (p = 0.027) and decreased expression of GK2 in HGSOC tissue from African ancestry women (p = 0.004). A European ancestry-derived polygenic risk score showed positive associations with EOC and HGSOC in women of African ancestry suggesting shared genetic architecture. Our investigation presents evidence of variants for EOC shared among European and African ancestry women and identifies novel EOC risk loci in women of African ancestry.
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Affiliation(s)
- Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Lauren C. Peres
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Xin-Qun Wang
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Mollie E. Barnard
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Deanna Chyn
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Zhaohui Du
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Jonathan Tyrer
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Joseph Dennis
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ann G. Schwartz
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI
| | - Michele L. Cote
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI
| | - Edward Peters
- Epidemiology Program, Louisiana State University Health Sciences Center School of Public Health, New Orleans, LA
| | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Melissa Bondy
- Cancer Prevention and Population Sciences Program, Baylor College of Medicine, Houston, TX
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Paul Terry
- Department of Medicine, University of Tennessee Medical Center – Knoxville, Knoxville, TN
| | - Anthony J. Alberg
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC
| | - Elisa V. Bandera
- Department of Population Science, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Ellen Funkhouser
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Malcom Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Roberta Ness
- The University of Texas School of Public Health, Houston, TX
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Beth Y. Karlan
- Department of Obstetrics and Gynecology, Ronald Regan UCLA Medical Center, Los Angeles, CA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Valerie McGuire
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, NY, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York
| | - Kate Lawrenson
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars-Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Paul Pharoah
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
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25
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Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma Using cis-eQTL Analysis. J Clin Med 2020; 9:jcm9041137. [PMID: 32316112 PMCID: PMC7231141 DOI: 10.3390/jcm9041137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023] Open
Abstract
Ovarian clear cell adenocarcinoma (Ov-CCA) has a higher prevalence in the Japanese ancestry than other populations. The ancestral disparities in Ov-CCA prevalence suggests the presence of Ov-CCA-specific genetic alterations and may provide an opportunity to identify the novel genes associated with Ov-CCA tumorigenesis. Using 94 previously reported genes as the phenotypic trait, we conducted multistep expression quantitative trait loci (eQTL) analysis with the HapMap3 project datasets. Four single-nucleotide polymorphisms (SNPs) (rs4873815, rs12976454, rs11136002, and rs13259097) that had different allele frequencies in the Japanese ancestry and seven genes associated in cis (APBA3, C8orf58, KIAA1967, NAPRT1, RHOBTB2, TNFRSF10B, and ZNF707) were identified. In silico functional annotation analysis and in vitro promoter assay validated the regulatory effect of rs4873815-TT on ZNF707 and rs11136002-TT on TNFRSF10B. Furthermore, ZNF707 was highly expressed in Ov-CCA and had a negative prognostic value in disease recurrence in our sample cohort. This prognostic power was consistently observed in The Cancer Genome Atlas (TCGA) clear cell renal cell carcinoma dataset, suggesting that ZNF707 may have prognostic value in clear cell histology regardless of tissue origin. In conclusion, rs4873815-TT/ZNF707 may have clinical significance in the prognosis and tumorigenesis of Ov-CCA, which may be more relevant to clear cell histology. Besides, this study may underpin the evidence that cis-eQTL analysis based on ancestral disparities can facilitate the discovery of causal genetic alterations in complex diseases, such as cancer.
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Zhou Z, Ou X, Zou Q, Chu L, Quan X, Chen Y, Liu Y. Functional polymorphisms in FOXC2 gene and Epithelial ovarian Cancer susceptibility in Chinese population. J Ovarian Res 2020; 13:34. [PMID: 32222147 PMCID: PMC7103066 DOI: 10.1186/s13048-020-00634-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Background Epithelial ovarian cancer (EOC) is highly lethal gynecological cancer. Forkhead Box Protein C2 (FOXC2) promotes occurrence and development of various malignant tumors. The present study is aimed at exploring the correlation between the polymorphism of FOXC2 and epithelial ovarian cancer susceptibility in Chinese Han population. Methods A case-control design was used to verify the association between FOXC2 polymorphisms and epithelial ovarian cancer. The genotyping was performed using Taqman® SNP Genotyping kit by qRT-PCR. The genetic variants including rs3751794 C > T, rs1035550 A > G, rs4843163 C > G and rs4843396 C > T in FOXC2 gene were analyzed. The strength of the associations was detected using odds ratios and 95% confidence intervals. Stratification analyses showed the association between the FOXC2 gene polymorphisms rs3751794 C > T, rs4843163 C > G and rs4843396 C > T with epithelial ovarian cancer susceptibility in terms of age, metastasis status, clinical stage, pathological grade, pregnant times, pausimenia, and the expression of ER, PR, wild p53 and mutant p53. Results Rs3751794 C > T (P = 0.0016), rs4843163 C > G (P < 0.0001) and rs4843396 C > T (P < 0.0001) were significantly associated with increased epithelial ovarian cancer risk. In stratification analyses,rs3751794 C > T, was identified to be dominant in no metastasis patients, clinical stage 4 group, middle grade pathological stage, pregnant time over 3 patients, post-menopause women, strong wild type p53 expression; rs4843163 C > G was dominant in high grade clinical stage, high grade pathological stage, post-menopause women, strong ER expression group and no mutant p53 expression group; rs4843396 C > T was dominant in high grade clinical stage, high grade pathological stage, strong ER expression group. The rs1035550 A > G was not related to epithelial ovarian cancer susceptibility. Conclusions The results of the current study verified that FOXC2 gene polymorphisms were associated with increased epithelial ovarian cancer risk and suggested that FOXC2 gene polymorphisms might be a potential biomarker for epithelial ovarian cancer susceptibility.
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Affiliation(s)
- Zhijiao Zhou
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Xiang Ou
- Department of Endocrinology, The First Hospital of Changsha, Changsha, Hunan, China
| | - Qiong Zou
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Ling Chu
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China
| | - Xiyun Quan
- Department of Pathology, Zhuzhou Central Hospital, Zhuzhou, Hunan, China
| | - Yong Chen
- Department of Clinical Laboratory, The First Hospital of Changsha, Changsha, Hunan, China
| | - Yang Liu
- Department of Pathology, Third Xiangya Hospital,Central South University, Changsha, 410013, Hunan, China.
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27
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Zhang L, Zhang Y, Wang S, Tao L, Pang L, Fu R, Fu Y, Liang W, Li F, Jia W. MiR-212-3p suppresses high-grade serous ovarian cancer progression by directly targeting MAP3K3. Am J Transl Res 2020; 12:875-888. [PMID: 32269720 PMCID: PMC7137041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 02/09/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are small regulatory non-coding RNAs that have been reported to play an important role in the tumorigenesis of many cancers. In addition, miRNAs might serve as new promising biomarkers for diagnosis and prognosis and as effective therapeutic targets for patients with such malignancies. Accordingly, the dysregulation of miR-212-3p has been reported in a variety of human cancers. However, its biological functions and molecular mechanisms high-grade serous ovarian cancer (HGSOG) remain unknown. In this study, we demonstrated that miR-212-3p interacts with MAP3K3 based on bioinformatics-based predictions. Further, MAP3K3 was identified as a direct target gene of miR-212-3p in HGSOC. In addition, overexpression of miR-212-3p in HGSOC inhibited cell proliferation, colony formation, invasion, and migration. In contrast MAP3K3 mitigated the suppressive effects of miR-212-3p on HGSOC cell proliferation, invasion, and migration. Furthermore, miR-212-3p was significantly downregulated in HGSOC tissues compared to expression in normal fallopian tube tissues and was inversely associated with MAP3K3 levels. Accordingly, low miR-212-3p expression was also correlated with poor prognosis for HGSOC patients. In conclusion, miR-212-3p might act as a suppressor of HGSOC carcinogenesis by directly targeting MAP3K3. Therefore, this miRNA could be a novel and effective target for the treatment of patients with HGSOC.
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Affiliation(s)
- Lu Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Ying Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Shasha Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Lin Tao
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Lijuan Pang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Ruiting Fu
- Department of Obestetrics and Gynecology, The First Affiliated Hospital School of Medicine, Shihezi UniversityShihezi, China
| | - Yu Fu
- Department of Obestetrics and Gynecology, The First Affiliated Hospital School of Medicine, Shihezi UniversityShihezi, China
| | - Weihua Liang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
| | - Feng Li
- Department of Pathology, Beijing Chaoyang HospitalBeijing, China
| | - Wei Jia
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of MedicineShihezi, China
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28
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Lyra PCM, Rangel LB, Monteiro ANA. Functional Landscape of Common Variants Associated with Susceptibility to Epithelial Ovarian Cancer. CURR EPIDEMIOL REP 2020. [DOI: 10.1007/s40471-020-00227-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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