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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 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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Xu F, Chen A, Pan S, Wu Y, He H, Han Z, Lu L, Orgil B, Chi X, Yang C, Jia S, Yu C, Mi J. Systems genetics analysis reveals the common genetic basis for pain sensitivity and cognitive function. CNS Neurosci Ther 2024; 30:e14557. [PMID: 38421132 PMCID: PMC10850811 DOI: 10.1111/cns.14557] [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: 07/11/2023] [Revised: 10/31/2023] [Accepted: 11/25/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND There is growing evidence of a strong correlation between pain sensitivity and cognitive function under both physiological and pathological conditions. However, the detailed mechanisms remain largely unknown. In the current study, we sought to explore candidate genes and common molecular mechanisms underlying pain sensitivity and cognitive function with a transcriptome-wide association study using recombinant inbred mice from the BXD family. METHODS The pain sensitivity determined by Hargreaves' paw withdrawal test and cognition-related phenotypes were systematically analyzed in 60 strains of BXD mice and correlated with hippocampus transcriptomes, followed by quantitative trait locus (QTL) mapping and systems genetics analysis. RESULTS The pain sensitivity showed significant variability across the BXD strains and co-varies with cognitive traits. Pain sensitivity correlated hippocampual genes showed a significant involvement in cognition-related pathways, including glutamatergic synapse, and PI3K-Akt signaling pathway. Moreover, QTL mapping identified a genomic region on chromosome 4, potentially regulating the variation of pain sensitivity. Integrative analysis of expression QTL mapping, correlation analysis, and Bayesian network modeling identified Ring finger protein 20 (Rnf20) as the best candidate. Further pathway analysis indicated that Rnf20 may regulate the expression of pain sensitivity and cognitive function through the PI3K-Akt signaling pathway, particularly through interactions with genes Ppp2r2b, Ppp2r5c, Col9a3, Met, Rps6, Tnc, and Kras. CONCLUSIONS Our study demonstrated that pain sensitivity is associated with genetic background and Rnf20-mediated PI3K-Akt signaling may involve in the regulation of pain sensitivity and cognitive functions.
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Affiliation(s)
- Fuyi Xu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Anran Chen
- The Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Shuijing Pan
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Yingying Wu
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Hongjie He
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Zhe Han
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Lu Lu
- University of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - XiaoDong Chi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Cunhua Yang
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
| | - Shushan Jia
- Department of AnesthesiologyYanTai Affiliated Hospital of BinZhou Medical UniversityYantaiChina
| | - Cuicui Yu
- The Affiliated Yantai Yuhuangding Hospital of Qingdao UniversityYantaiChina
| | - Jia Mi
- Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and TreatmentBinzhou Medical UniversityYantaiChina
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3
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Xiao Q, Mears J, Nathan A, Ishigaki K, Baglaenko Y, Lim N, Cooney LA, Harris KM, Anderson MS, Fox DA, Smilek DE, Krueger JG, Raychaudhuri S. Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin. Nat Commun 2023; 14:6268. [PMID: 37805522 PMCID: PMC10560299 DOI: 10.1038/s41467-023-41984-2] [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: 10/13/2022] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
Psoriasis is a chronic, systemic inflammatory condition primarily affecting skin. While the role of the immune compartment (e.g., T cells) is well established, the changes in the skin compartment are more poorly understood. Using longitudinal skin biopsies (n = 375) from the "Psoriasis Treatment with Abatacept and Ustekinumab: A Study of Efficacy"(PAUSE) clinical trial (n = 101), we report 953 expression quantitative trait loci (eQTLs). Of those, 116 eQTLs have effect sizes that were modulated by local skin inflammation (eQTL interactions). By examining these eQTL genes (eGenes), we find that most are expressed in the skin tissue compartment, and a subset overlap with the NRF2 pathway. Indeed, the strongest eQTL interaction signal - rs1491377616-LCE3C - links a psoriasis risk locus with a gene specifically expressed in the epidermis. This eQTL study highlights the potential to use biospecimens from clinical trials to discover in vivo eQTL interactions with therapeutically relevant environmental variables.
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Affiliation(s)
- Qian Xiao
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph Mears
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Noha Lim
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Laura A Cooney
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Internal Medicine and Clinical Autoimmunity Center of Excellence, University of Michigan, Ann Arbor, MI, USA
| | - Kristina M Harris
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - David A Fox
- Division of Rheumatology, Department of Internal Medicine and Clinical Autoimmunity Center of Excellence, University of Michigan, Ann Arbor, MI, USA
| | - Dawn E Smilek
- Immune Tolerance Network, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
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4
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Cho JM, Koh JH, Kim SG, Lee S, Kim Y, Cho S, Kim K, Kim YC, Han SS, Lee H, Lee JP, Joo KW, Lim CS, Kim YS, Kim DK, Park S. Mendelian randomization uncovers a protective effect of interleukin-1 receptor antagonist on kidney function. Commun Biol 2023; 6:722. [PMID: 37452175 PMCID: PMC10349143 DOI: 10.1038/s42003-023-05091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023] Open
Abstract
Interleukins (ILs), key cytokine family of inflammatory response, are closely associated with kidney function. However, the causal effect of various ILs on kidney function needs further investigation. Here we show two-sample summary-level Mendelian randomization (MR) analysis that examined the causality between serum IL levels and kidney function. Genetic variants with strong association with serum IL levels were obtained from a previous genome-wide association study meta-analysis. Summary-level data for estimated glomerular filtration rate (eGFR) were obtained from CKDGen database. As a main MR analysis, multiplicative random-effects inverse-variance weighted method was performed. Pleiotropy-robust MR analysis, including MR-Egger with bootstrapped error and weighted median methods, were also implemented. We tested the causal estimates from nine ILs on eGFR traits. Among the results, higher genetically predicted serum IL-1 receptor antagonist level was significantly associated with higher eGFR values in the meta-analysis of CKDGen and the UK Biobank data. In addition, the result was consistent towards eGFR decline phenotype of the outcome database. Otherwise, nonsignificant association was identified between other genetically predicted ILs and eGFR outcome. These findings support the clinical importance of IL-1 receptor antagonist-associated pathway in relation to kidney function in the general individuals, particularly highlighting the importance of IL-1 receptor antagonist.
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Affiliation(s)
- Jeong Min Cho
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jung Hun Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Seong Geun Kim
- Department of Internal Medicine, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Soojin Lee
- Department of Internal Medicine, Uijeongbu Eulji University Medical Center, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Semin Cho
- Department of Internal Medicine, Chung-Ang University Gwangmyeong Hospital, Gyeonggi-do, Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Yong Chul Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Pyo Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Kwon Wook Joo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Chun Soo Lim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Yon Su Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Sehoon Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
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5
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Zhang F, Jiao H, Wang Y, Yang C, Li L, Wang Z, Tong R, Zhou J, Shen J, Li L. InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop. Brief Bioinform 2023; 24:7150740. [PMID: 37139553 DOI: 10.1093/bib/bbad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/21/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023] Open
Abstract
Deciphering cell-type-specific 3D structures of chromatin is challenging. Here, we present InferLoop, a novel method for inferring the strength of chromatin interaction using single-cell chromatin accessibility data. The workflow of InferLoop is, first, to conduct signal enhancement by grouping nearby cells into bins, and then, for each bin, leverage accessibility signals for loop signals using a newly constructed metric that is similar to the perturbation of the Pearson correlation coefficient. In this study, we have described three application scenarios of InferLoop, including the inference of cell-type-specific loop signals, the prediction of gene expression levels and the interpretation of intergenic loci. The effectiveness and superiority of InferLoop over other methods in those three scenarios are rigorously validated by using the single-cell 3D genome structure data of human brain cortex and human blood, the single-cell multi-omics data of human blood and mouse brain cortex, and the intergenic loci in the GWAS Catalog database as well as the GTEx database, respectively. In addition, InferLoop can be applied to predict loop signals of individual spots using the spatial chromatin accessibility data of mouse embryo. InferLoop is available at https://github.com/jumphone/inferloop.
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Affiliation(s)
- Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huiyuan Jiao
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yihao Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai 201109, China
| | - Chen Yang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Linying Li
- Department of Central Laboratory, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhiming Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ran Tong
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Junmei Zhou
- Department of Central Laboratory, Shanghai Children's Hospital, School of medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai 201109, China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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6
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Punzón-Jiménez P, Lago V, Domingo S, Simón C, Mas A. Molecular Management of High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:13777. [PMID: 36430255 PMCID: PMC9692799 DOI: 10.3390/ijms232213777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) represents the most common form of epithelial ovarian carcinoma. The absence of specific symptoms leads to late-stage diagnosis, making HGSOC one of the gynecological cancers with the worst prognosis. The cellular origin of HGSOC and the role of reproductive hormones, genetic traits (such as alterations in P53 and DNA-repair mechanisms), chromosomal instability, or dysregulation of crucial signaling pathways have been considered when evaluating prognosis and response to therapy in HGSOC patients. However, the detection of HGSOC is still based on traditional methods such as carbohydrate antigen 125 (CA125) detection and ultrasound, and the combined use of these methods has yet to support significant reductions in overall mortality rates. The current paradigm for HGSOC management has moved towards early diagnosis via the non-invasive detection of molecular markers through liquid biopsies. This review presents an integrated view of the relevant cellular and molecular aspects involved in the etiopathogenesis of HGSOC and brings together studies that consider new horizons for the possible early detection of this gynecological cancer.
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Affiliation(s)
- Paula Punzón-Jiménez
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
| | - Victor Lago
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Obstetrics and Gynecology, CEU Cardenal Herrera University, 46115 Valencia, Spain
| | - Santiago Domingo
- Department of Gynecologic Oncology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
| | - Carlos Simón
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Universidad de Valencia, 46010 Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Harvard University, Boston, MA 02215, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aymara Mas
- Carlos Simon Foundation, INCLIVA Health Research Institute, 46010 Valencia, Spain
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Long Noncoding RNA LINC00909 Induces Epithelial-Mesenchymal Transition and Contributes to Osteosarcoma Tumorigenesis and Metastasis. JOURNAL OF ONCOLOGY 2022; 2022:8660965. [PMID: 36262353 PMCID: PMC9576421 DOI: 10.1155/2022/8660965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022]
Abstract
Background Osteosarcoma (OS) is a malignant tumor that is highly metastatic with a high mortality rate. Although mounting evidence suggests that LINC00909 is strongly associated with the malignant progression of various tumors, the exact role of LINC00909 in OS remains unknown. Therefore, the current study was designed to investigate the relationship between LINC00909 and the malignant progression of OS. Methods LINC00909 expression was measured in OS cell lines and clinical specimens using RT-qPCR assays. The effects of LINC00909 on OS proliferation, invasion, and migration were calculated both in vitro and in vivo. Apart from that, bioinformatics analyses, FISH, RIP, and luciferase reporter assays were carried out to investigate the downstream target of LINC00909. Rescue experiments were also conducted to investigate the potential mechanisms of action of competitive endogenous RNAs (ceRNAs). Results In this study, we found that LINC00909 was highly expressed in OS cell lines and clinical specimens. In vivo and in vitro experiments demonstrated that LINC00909 induces epithelial-to-mesenchymal transition (EMT) and contributes to OS tumorigenesis and metastasis. FISH, RIP, and luciferase assays indicated that miR-875-5p is a direct target of LINC00909. Moreover, HOXD9 was validated as the downstream target of miR-875-5p in a luciferase reporter assay and western blotting experiments. Rescue experiments revealed that HOXD9 reversed the effect of LV-sh-LINC00909 on OS cells by positively regulating the PI3K/AKT/mTOR signaling pathway. Conclusion Collectively, LINC00909 induces EMT and contributes to OS tumorigenesis and metastasis through the PI3K/AKT/mTOR pathway by binding to miR-875-5p to upregulate HOXD9 expression. Targeting the LINC00909/miR-875-5p/HOXD9 axis may have potential in treating OS.
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8
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Nameki R, Shetty A, Dareng E, Tyrer J, Lin X, Pharoah P, Corona RI, Kar S, Lawrenson K. chromMAGMA: regulatory element-centric interrogation of risk variants. Life Sci Alliance 2022; 5:e202201446. [PMID: 35777959 PMCID: PMC9251535 DOI: 10.26508/lsa.202201446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Candidate causal risk variants from genome-wide association studies reside almost exclusively in noncoding regions of the genome and innovative approaches are necessary to understand their biological function. Multi-marker analysis of genomic annotation (MAGMA) is a widely used program that nominates candidate risk genes by mapping single-nucleotide polymorphism summary statistics from genome-wide association studies to gene bodies. We augmented MAGMA to create chromatin-MAGMA (chromMAGMA), a method to nominate candidate risk genes based on the presence of risk variants within noncoding regulatory elements (REs). We applied chromMAGMA to a genetic susceptibility dataset for epithelial ovarian cancer (EOC), a rare gynecologic malignancy characterized by high mortality. This identified 155 unique candidate EOC risk genes across five EOC histotypes; 83% (105/127) of high-grade serous ovarian cancer risk genes had not previously been implicated in this EOC histotype. Risk genes nominated by chromMAGMA converged on mRNA splicing and transcriptional dysregulation pathways. chromMAGMA is a pipeline that nominates candidate risk genes through a gene regulation-focused approach and helps interpret the biological mechanism of noncoding risk variants for complex diseases.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Anamay Shetty
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eileen Dareng
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan Tyrer
- 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
| | - Xianzhi Lin
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Paul 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
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
- Cancer Prevention and Control Program, Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Zafar A, Shafiq M, Ali B, Sadee W, Shakoori AR, Shakoori FR. Association of IRGM promoter region polymorphisms and haplotype with pulmonary tuberculosis in Pakistani (Punjab) population. Tuberculosis (Edinb) 2022; 136:102233. [DOI: 10.1016/j.tube.2022.102233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
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10
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Wu XC, Yu YZ, Zuo YZ, Song XL, Zhou ZE, Xiao Y, Luo DS, Yan WG, Zhao SC. Identification of UAP1L1 as a critical factor for prostate cancer and underlying molecular mechanism in tumorigenicity. J Transl Med 2022; 20:91. [PMID: 35168617 PMCID: PMC8845250 DOI: 10.1186/s12967-022-03291-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/02/2022] [Indexed: 12/24/2022] Open
Abstract
Background Prostate cancer is the second most common cancer in men, and some new target genes are needed to predict the risk of prostate cancer progression and the treatment. Methods In this study, the effects of UAP1L1 (UAP1-like-1) on prostate cancer were investigated by detecting the proliferation, migration, invasion and apoptosis of prostate cancer cells in vitro using MTT, wound healing, Transwell and flow cytometry assay, and the tumor growth in vivo. The downstream genes and pathways of UAP1L1 were explored using Ingenuity Pathway Analysis (IPA), and screened by qRT-PCR and western blot. The effects of CDCA8 on prostate cancer cells were also verified in vitro, which was through detecting the change of proliferation, migration, invasion and apoptosis of prostate cancer cells after CDCA8 knockdown. Results The results indicated that UAP1L1 promoted the proliferation, migration and invasion of prostate cancer cells, which was inhibited by downregulating CDCA8. Furthermore, the promotion of CDCA8 knockdown on cell apoptosis was reduced when UAP1L1 was simultaneously overexpressed. Conclusions In conclusion, the results in this study revealed that UAP1L1 promoted the progression of prostate cancer through the downstream gene CDCA8. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03291-0.
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Affiliation(s)
- Xing-Cheng Wu
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100720, China
| | - Yu-Zhong Yu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yu-Zhi Zuo
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100720, China
| | - Xian-Lu Song
- Department of Radiotherapy, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhi-En Zhou
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100720, China
| | - Yu Xiao
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dao-Sheng Luo
- Department of Urology, Dongguan Hospital, Southern Medical University, Guangzhou, China
| | - Wei-Gang Yan
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100720, China.
| | - Shan-Chao Zhao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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11
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Genome and transcriptome profiling of spontaneous preterm birth phenotypes. Sci Rep 2022; 12:1003. [PMID: 35046466 PMCID: PMC8770724 DOI: 10.1038/s41598-022-04881-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/23/2021] [Indexed: 12/27/2022] Open
Abstract
Preterm birth (PTB) occurs before 37 weeks of gestation. Risk factors include genetics and infection/inflammation. Different mechanisms have been reported for spontaneous preterm birth (SPTB) and preterm birth following preterm premature rupture of membranes (PPROM). This study aimed to identify early pregnancy biomarkers of SPTB and PPROM from the maternal genome and transcriptome. Pregnant women were recruited at the Liverpool Women’s Hospital. Pregnancy outcomes were categorised as SPTB, PPROM (≤ 34 weeks gestation, n = 53), high-risk term (HTERM, ≥ 37 weeks, n = 126) or low-risk (no history of SPTB/PPROM) term (LTERM, ≥ 39 weeks, n = 188). Blood samples were collected at 16 and 20 weeks gestation from which, genome (UK Biobank Axiom array) and transcriptome (Clariom D Human assay) data were acquired. PLINK and R were used to perform genetic association and differential expression analyses and expression quantitative trait loci (eQTL) mapping. Several significant molecular signatures were identified across the analyses in preterm cases. Genome-wide significant SNP rs14675645 (ASTN1) was associated with SPTB whereas microRNA-142 transcript and PPARG1-FOXP3 gene set were associated with PPROM at week 20 of gestation and is related to inflammation and immune response. This study has determined genomic and transcriptomic candidate biomarkers of SPTB and PPROM that require validation in diverse populations.
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12
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Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth FA. Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. Am J Hum Genet 2022; 109:116-135. [PMID: 34965383 DOI: 10.1016/j.ajhg.2021.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022] Open
Abstract
The high-grade serous ovarian cancer (HGSOC) risk locus at chromosome 1p34.3 resides within a frequently amplified genomic region signifying the presence of an oncogene. Here, we integrate in silico variant-to-function analysis with functional studies to characterize the oncogenic potential of candidate genes in the 1p34.3 locus. Fine mapping of genome-wide association statistics identified candidate causal SNPs local to H3K27ac-demarcated enhancer regions that exhibit allele-specific binding for CTCF in HGSOC and normal fallopian tube secretory epithelium cells (FTSECs). SNP risk associations colocalized with eQTL for six genes (DNALI1, GNL2, RSPO1, SNIP1, MEAF6, and LINC01137) that are more highly expressed in carriers of the risk allele, and three (DNALI1, GNL2, and RSPO1) were upregulated in HGSOC compared to normal ovarian surface epithelium cells and/or FTSECs. Increased expression of GNL2 and MEAF6 was associated with shorter survival in HGSOC with 1p34.3 amplifications. Despite its activation of β-catenin signaling, RSPO1 overexpression exerted no effects on proliferation or colony formation in our study of ovarian cancer and FTSECs. Instead, GNL2, MEAF6, and SNIP1 silencing impaired in vitro ovarian cancer cell growth. Additionally, GNL2 silencing diminished xenograft tumor formation, whereas overexpression stimulated proliferation and colony formation in FTSECs. GNL2 influences 60S ribosomal subunit maturation and global protein synthesis in ovarian cancer and FTSECs, providing a potential mechanism of how GNL2 upregulation might promote ovarian cancer development and mediate genetic susceptibility of HGSOC.
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13
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Peres LC, Monteiro AN. Scratching Below the Ovarian Cancer GWAS Surface. Cancer Epidemiol Biomarkers Prev 2021; 30:1604-1606. [PMID: 34475121 DOI: 10.1158/1055-9965.epi-21-0568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/12/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022] Open
Abstract
Despite recent notable treatment advancements, ovarian cancer survival rates remain poor, with about half of women surviving five years after diagnosis. Uncovering novel prognostic factors is critical to better understand and reduce mortality from this deadly disease. While genome-wide association studies have identified numerous loci associated with risk of epithelial ovarian cancer, the investigation of genetic factors associated with outcomes among women with ovarian cancer has been limited due to several challenges summarized in the present commentary. Using data from the Ovarian Cancer Association Consortium, Quinn and colleagues conducted a genome-wide association study of patients with ovarian cancer receiving debulking surgery and standard chemotherapy as first-line treatment, revealing a locus at 12q24.33 associated with progression-free survival. Experimental evidence suggests that ULK1, a gene coding for a serine/threonine kinase implicated in autophagy, is the target of the association. We discuss the novelty of these findings, unanswered questions, and next steps for the road ahead in translating the work of Quinn and colleagues into clinical practice.See related article by Quinn et al., p. 1669.
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Affiliation(s)
- Lauren C Peres
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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14
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Spirko-Burns L, Devarajan K. Supervised Dimension Reduction for Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2032-2044. [PMID: 31940547 DOI: 10.1109/tcbb.2020.2965934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The past two decades have witnessed significant advances in high-throughput "omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive "omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential time-varying effects of features, and methods for handling them have been lacking. In this paper, we propose supervised methods for feature selection and survival prediction that simultaneously deal with both issues. Our approach utilizes continuum power regression (CPR) - a framework that includes a variety of regression methods - in conjunction with the parametric or semi-parametric accelerated failure time (AFT) model. Both CPR and AFT fall within the linear models framework and, unlike black-box models, the proposed prognostic index has a simple yet useful interpretation. We demonstrate the utility of our methods using simulated and publicly available cancer genomics data.
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15
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Dash S, Yoder S, Mesa T, Smith A, Cen L, Eschrich S, Armaiz-Pena GN, Monteiro ANA. Effects of long-term norepinephrine treatment on normal immortalized ovarian and fallopian tube cells. Sci Rep 2021; 11:14334. [PMID: 34253763 PMCID: PMC8275603 DOI: 10.1038/s41598-021-93506-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/24/2021] [Indexed: 11/08/2022] Open
Abstract
Sustained adrenergic stimulation by norepinephrine (NE) contributes to ovarian carcinoma metastasis and impairment of chemotherapy response. Although the effect of sustained NE stimulation in cancer progression is well established, less is known about its role in cancer initiation. To determine the extent to which stress hormones influence ovarian cancer initiation, we conducted a long-term (> 3 months; > 40 population doublings) experiment in which normal immortalized fallopian tube secretory (iFTSEC283) and ovarian surface epithelial (iOSE11) cell lines and their isogenic pairs containing a p53 mutation (iFTSEC283p53R175H; iOSE11p53R175H), were continuously exposed to NE (100 nM, 1 μM, 10 μM). Fallopian tube cells displayed a p53-independent increase in proliferation and colony-forming ability in response to NE, while ovarian surface epithelial cells displayed a p53-independent decrease in both assays. Fallopian tube cells with mutant p53 showed a mild loss of chromosomes and TP53 status was also a defining factor in transcriptional response of fallopian tube cells to long-term NE treatment.
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Affiliation(s)
- Sweta Dash
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Magnolia Drive, Tampa, FL, 1290233612, USA
- Cancer Biology Ph.D. Program, University of South Florida Tampa, Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Tania Mesa
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Andrew Smith
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ling Cen
- Data Sharing Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Steven Eschrich
- Data Sharing Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Guillermo N Armaiz-Pena
- Department of Basic Sciences, Pharmacology Division, School of Medicine, Ponce Health Sciences University and Divisions of Cancer Biology and Women's Health, Ponce Research Institute, Ponce, PR, USA
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Magnolia Drive, Tampa, FL, 1290233612, USA.
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16
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Nameki R, Chang H, Reddy J, Corona RI, Lawrenson K. Transcription factors in epithelial ovarian cancer: histotype-specific drivers and novel therapeutic targets. Pharmacol Ther 2020; 220:107722. [PMID: 33137377 DOI: 10.1016/j.pharmthera.2020.107722] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) are major contributors to cancer risk and somatic development. In preclinical and clinical studies, direct or indirect inhibition of TF-mediated oncogenic gene expression profiles have proven to be effective in many tumor types, highlighting this group of proteins as valuable therapeutic targets. In spite of this, our understanding of TFs in epithelial ovarian cancer (EOC) is relatively limited. EOC is a heterogeneous disease composed of five major histologic subtypes; high-grade serous, low-grade serous, endometrioid, clear cell and mucinous. Each histology is associated with unique clinical etiologies, sensitivity to therapies, and molecular signatures - including diverse transcriptional regulatory programs. While some TFs are shared across EOC subtypes, a set of TFs are expressed in a histotype-specific manner and likely explain part of the histologic diversity of EOC subtypes. Targeting TFs present with unique opportunities for development of novel precision medicine strategies for ovarian cancer. This article reviews the critical TFs in EOC subtypes and highlights the potential of exploiting TFs as biomarkers and therapeutic targets.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Heidi Chang
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Jessica Reddy
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, 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; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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17
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Li W, Xu C, Guo J, Liu K, Hu Y, Wu D, Fang H, Zou Y, Wei Z, Wang Z, Zhou Y, Li Q. Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications. Front Oncol 2020; 10:602104. [PMID: 33194770 PMCID: PMC7604522 DOI: 10.3389/fonc.2020.602104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are enriched in the immune system processes and eQTL-elncRNA associations influence the constitution of tumor infiltrating lymphocytes. In ovarian cancer, the "rs34631313-AC092580.4" pair was associated with increased fraction of CD8+ T cells and M1 Macrophage; whereas in KIRC, the "rs9546285-LINC00426" pair was associated with increased fraction of CD8+ T cells and a decreased fraction of M2 macrophages. Our findings provide a systematic view of the transcriptomic impacts of the eQTL landscape of lncRNA in human cancers and suggest its strong potential relevance to cancer immunity and treatment.
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Affiliation(s)
- Wenzhi Li
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoqun Xu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jintao Guo
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Ke Liu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yudi Hu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Dan Wu
- Department of Oncology, Xiamen the Fifth Hospital, Xiamen, China
| | - Hongkun Fang
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yun Zou
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziwei Wei
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhou
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
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18
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Liu Y, Liu X, Zheng Z, Ma T, Liu Y, Long H, Cheng H, Fang M, Gong J, Li X, Zhao S, Xu X. Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits. Genet Sel Evol 2020; 52:59. [PMID: 33036552 PMCID: PMC7547458 DOI: 10.1186/s12711-020-00579-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 09/28/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. RESULTS Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). CONCLUSIONS The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.
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Affiliation(s)
- Yan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Zhiwei Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Tingting Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Ying Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Huan Long
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Huijun Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Ming Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, 361021 China
| | - Jing Gong
- Colleges of Informatics, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 China
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070 China
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19
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Jones MR, Peng PC, Coetzee SG, Tyrer J, Reyes ALP, Corona RI, Davis B, Chen S, Dezem F, Seo JH, Kar S, Dareng E, Berman BP, Freedman ML, Plummer JT, Lawrenson K, Pharoah P, Hazelett DJ, Gayther SA. Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. Am J Hum Genet 2020; 107:622-635. [PMID: 32946763 PMCID: PMC7536645 DOI: 10.1016/j.ajhg.2020.08.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/15/2020] [Indexed: 12/14/2022] Open
Abstract
Quantifying the functional effects of complex disease risk variants can provide insights into mechanisms underlying disease biology. Genome-wide association studies have identified 39 regions associated with risk of epithelial ovarian cancer (EOC). The vast majority of these variants lie in the non-coding genome, where they likely function through interaction with gene regulatory elements. In this study we first estimated the heritability explained by known common low penetrance risk alleles for EOC. The narrow sense heritability (hg2) of EOC overall and high-grade serous ovarian cancer (HGSOCs) were estimated to be 5%-6%. Partitioned SNP heritability across broad functional categories indicated a significant contribution of regulatory elements to EOC heritability. We collated epigenomic profiling data for 77 cell and tissue types from Roadmap Epigenomics and ENCODE, and from H3K27Ac ChIP-seq data generated in 26 ovarian cancer and precursor-related cell and tissue types. We identified significant enrichment of risk single-nucleotide polymorphisms (SNPs) in active regulatory elements marked by H3K27Ac in HGSOCs. To further investigate how risk SNPs in active regulatory elements influence predisposition to ovarian cancer, we used motifbreakR to predict the disruption of transcription factor binding sites. We identified 469 candidate causal risk variants in H3K27Ac peaks that are predicted to significantly break transcription factor (TF) motifs. The most frequently broken motif was REST (p value = 0.0028), which has been reported as both a tumor suppressor and an oncogene. Overall, these systematic functional annotations with epigenomic data improve interpretation of EOC risk variants and shed light on likely cells of origin.
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Affiliation(s)
- Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Pei-Chen Peng
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Simon G Coetzee
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jonathan Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Alberto Luiz P Reyes
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rosario I Corona
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Brian Davis
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Felipe Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Siddartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Eileen Dareng
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 9112102, Israel
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jasmine T Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Dennis J Hazelett
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Matos MR, Ho SM, Schrode N, Brennand KJ. Integration of CRISPR-engineering and hiPSC-based models of psychiatric genomics. Mol Cell Neurosci 2020; 107:103532. [PMID: 32712198 PMCID: PMC7484226 DOI: 10.1016/j.mcn.2020.103532] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023] Open
Abstract
Neuropsychiatric disorders are highly heritable polygenic disorders arising from the complex interplay of highly penetrant rare variants and common variants of small effect. There is a large index of comorbidity and shared genetic risk between disorders, reflecting the pleiotropy of individual variants as well as predicted downstream pathway-level convergence. Importantly, the mechanism(s) through which psychiatric disease-associated variants interact to contribute to disease risk remains unknown. Human induced pluripotent stem cell (hiPSC)-based models are increasingly useful for the systematic study of the complex genetics associated with brain diseases, particularly when combined with CRISPR-mediated genomic engineering, which together facilitate isogenic comparisons of defined neuronal cell types. In this review, we discuss the latest CRISPR technologies and consider how they can be successfully applied to the functional characterization of the growing list genetic variants linked to psychiatric disease.
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Affiliation(s)
- Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Seok-Man Ho
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
| | - Nadine Schrode
- Department of Genetics and Genomics, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America.
| | - Kristen J Brennand
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Genetics and Genomics, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America.
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21
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Corona RI, Seo JH, Lin X, Hazelett DJ, Reddy J, Fonseca MAS, Abassi F, Lin YG, Mhawech-Fauceglia PY, Shah SP, Huntsman DG, Gusev A, Karlan BY, Berman BP, Freedman ML, Gayther SA, Lawrenson K. Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer. Nat Commun 2020; 11:2020. [PMID: 32332753 PMCID: PMC7181647 DOI: 10.1038/s41467-020-15951-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The functional consequences of somatic non-coding mutations in ovarian cancer (OC) are unknown. To identify regulatory elements (RE) and genes perturbed by acquired non-coding variants, here we establish epigenomic and transcriptomic landscapes of primary OCs using H3K27ac ChIP-seq and RNA-seq, and then integrate these with whole genome sequencing data from 232 OCs. We identify 25 frequently mutated regulatory elements, including an enhancer at 6p22.1 which associates with differential expression of ZSCAN16 (P = 6.6 × 10-4) and ZSCAN12 (P = 0.02). CRISPR/Cas9 knockout of this enhancer induces downregulation of both genes. Globally, there is an enrichment of single nucleotide variants in active binding sites for TEAD4 (P = 6 × 10-11) and its binding partner PAX8 (P = 2×10-10), a known lineage-specific transcription factor in OC. In addition, the collection of cis REs associated with PAX8 comprise the most frequently mutated set of enhancers in OC (P = 0.003). These data indicate that non-coding somatic mutations disrupt the PAX8 transcriptional network during OC development.
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Affiliation(s)
- Rosario I Corona
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xianzhi Lin
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Dennis J Hazelett
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Forough Abassi
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Yvonne G Lin
- Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Sohrab P Shah
- Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, BC, Canada
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Beth Y Karlan
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
| | - Simon A Gayther
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Kate Lawrenson
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA.
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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22
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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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23
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A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine. Trends Genet 2020; 36:318-336. [PMID: 32294413 DOI: 10.1016/j.tig.2020.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 02/07/2023]
Abstract
Quantitative trait loci (QTL) analysis is an important approach to investigate the effects of genetic variants identified through an increasing number of large-scale, multidimensional 'omics data sets. In this 'big data' era, the research community has identified a significant number of molecular QTLs (molQTLs) and increased our understanding of their effects. Herein, we review multiple categories of molQTLs, including those associated with transcriptome, post-transcriptional regulation, epigenetics, proteomics, metabolomics, and the microbiome. We summarize approaches to identify molQTLs and to infer their causal effects. We further discuss the integrative analysis of molQTLs through a multi-omics perspective. Our review highlights future opportunities to better understand the functional significance of genetic variants and to utilize the discovery of molQTLs in precision medicine.
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Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B. cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel. Genome Biol 2020; 21:6. [PMID: 31948474 PMCID: PMC6966807 DOI: 10.1186/s13059-019-1912-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited. RESULTS To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression. CONCLUSIONS Our collective findings point to a large number of infection-specific cis- and trans-acting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.
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Affiliation(s)
- Michael V. Frochaux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Riccardo Dainese
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brian Hollis
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Current Address: Department of Biological Sciences, University of South Carolina, Columbia, South Carolina USA
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Virginie S. Braman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Tommaso Andreani
- Computational Biology and Data Mining Group, Institute of Molecular Biology, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Dani Osman
- Faculty of Sciences III and Azm Center for Research in Biotechnology and its Applications, LBA3B, EDST, Lebanese University, Tripoli, 1300 Lebanon
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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25
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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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26
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Glubb DM, Shi W, Beesley J, Fachal L, Pritchard JL, McCue K, Barnes DR, Antoniou AC, Dunning AM, Easton DF, Chenevix-Trench G. Candidate Causal Variants at the 8p12 Breast Cancer Risk Locus Regulate DUSP4. Cancers (Basel) 2020; 12:E170. [PMID: 31936698 PMCID: PMC7016765 DOI: 10.3390/cancers12010170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/30/2019] [Indexed: 11/16/2022] Open
Abstract
Genome-wide association studies have revealed a locus at 8p12 that is associated with breast cancer risk. Fine-mapping of this locus identified 16 candidate causal variants (CCVs). However, as these variants are intergenic, their function is unclear. To map chromatin looping from this risk locus to a previously identified candidate target gene, DUSP4, we performed chromatin conformation capture analyses in normal and tumoural breast cell lines. We identified putative regulatory elements, containing CCVs, which looped to the DUSP4 promoter region. Using reporter gene assays, we found that the risk allele of CCV rs7461885 reduced the activity of a DUSP4 enhancer element, consistent with the function of DUSP4 as a tumour suppressor gene. Furthermore, the risk allele of CCV rs12155535, located in another DUSP4 enhancer element, was negatively correlated with looping of this element to the DUSP4 promoter region, suggesting that this allele would be associated with reduced expression. These findings provide the first evidence that CCV risk alleles downregulate DUSP4 expression, suggesting that this gene is a regulatory target of the 8p12 breast cancer risk locus.
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Affiliation(s)
- Dylan M. Glubb
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
| | - Wei Shi
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (L.F.); (A.M.D.); (D.F.E.)
| | - Jayne-Louise Pritchard
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
| | - Karen McCue
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
| | - Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (D.R.B.); (A.C.A.)
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (D.R.B.); (A.C.A.)
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (L.F.); (A.M.D.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (L.F.); (A.M.D.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (D.R.B.); (A.C.A.)
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD 4006, Australia; (W.S.); (J.B.); (J.-L.P.); (K.M.); (G.C.-T.)
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Ohishi H, Au Yeung WK, Unoki M, Ichiyanagi K, Fukuda K, Maenohara S, Shirane K, Chiba H, Sado T, Sasaki H. Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells. Genes Cells 2019; 25:54-64. [PMID: 31733167 DOI: 10.1111/gtc.12736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022]
Abstract
Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.
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Affiliation(s)
- Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN, Wako, Japan
| | - Shoji Maenohara
- Gynecology Service, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kenjiro Shirane
- Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Hatsune Chiba
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Sado
- Department of Advanced Bioscience, Graduate School of Agriculture, KINDAI University, Nara, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Gorlov I, Xiao X, Mayes M, Gorlova O, Amos C. SNP eQTL status and eQTL density in the adjacent region of the SNP are associated with its statistical significance in GWA studies. BMC Genet 2019; 20:85. [PMID: 31718536 PMCID: PMC6852916 DOI: 10.1186/s12863-019-0786-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/18/2019] [Indexed: 01/05/2023] Open
Abstract
Background Over the relatively short history of Genome Wide Association Studies (GWASs), hundreds of GWASs have been published and thousands of disease risk-associated SNPs have been identified. Summary statistics from the conducted GWASs are often available and can be used to identify SNP features associated with the level of GWAS statistical significance. Those features could be used to select SNPs from gray zones (SNPs that are nominally significant but do not reach the genome-wide level of significance) for targeted analyses. Methods We used summary statistics from recently published breast and lung cancer and scleroderma GWASs to explore the association between the level of the GWAS statistical significance and the expression quantitative trait loci (eQTL) status of the SNP. Data from the Genotype-Tissue Expression Project (GTEx) were used to identify eQTL SNPs. Results We found that SNPs reported as eQTLs were more significant in GWAS (higher -log10p) regardless of the tissue specificity of the eQTL. Pan-tissue eQTLs (those reported as eQTLs in multiple tissues) tended to be more significant in the GWAS compared to those reported as eQTL in only one tissue type. eQTL density in the ±5 kb adjacent region of a given SNP was also positively associated with the level of GWAS statistical significance regardless of the eQTL status of the SNP. We found that SNPs located in the regions of high eQTL density were more likely to be located in regulatory elements (transcription factor or miRNA binding sites). When SNPs were stratified by the level of statistical significance, the proportion of eQTLs was positively associated with the mean level of statistical significance in the group. The association curve reaches a plateau around -log10p ≈ 5. The observed associations suggest that quasi-significant SNPs (10− 5 < p < 5 × 10− 8) and SNPs at the genome wide level of statistical significance (p < 5 × 10− 8) may have a similar proportions of risk associated SNPs. Conclusions The results of this study indicate that the SNP’s eQTL status, as well as eQTL density in the adjacent region are positively associated with the level of statistical significance of the SNP in GWAS.
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Affiliation(s)
- Ivan Gorlov
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Xiangjun Xiao
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Maureen Mayes
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, USA
| | - Olga Gorlova
- The Geisel School of Medicine, Department of Biomedical Data Science, Dartmouth College, HB7936, One Medical Center Dr., Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Christopher Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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29
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Christophersen MK, Høgdall C, Høgdall E. The prospect of discovering new biomarkers for ovarian cancer based on current knowledge of susceptibility loci and genetic variation (Review). Int J Mol Med 2019; 44:1599-1608. [PMID: 31573049 DOI: 10.3892/ijmm.2019.4352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/30/2019] [Indexed: 11/05/2022] Open
Abstract
Ovarian cancer is the most lethal gynaecological malignancy. The cancer initially presents with non‑specific symptoms; thus, it is typically not discovered until the patient has reached the late, considerably more lethal, stages of the disease. Research focus is currently on finding novel biomarkers, especially for early detection and stratification of the disease. One promising approach has been to focus on mutations or variations in the genetic code that are associated with the risk of developing ovarian cancer. A certain heritable component is already known regarding genes such as BRCA1/2, TP53, MSH6, BRIP1 and RAD51C, yet these are estimated to only account for ~3.1% of the total risk. Recent advances in sequencing technologies have enabled the investigation of hundreds of thousands of genetic variants in genome‑wide association studies in tens of thousands of patients, which has led to the discovery of 108 (39 loci with P<5.0x10‑8) novel susceptibility loci for ovarian cancer, presented in this review. Using the published variants in a patient cohort screening, together with variants identified in our ongoing whole exome sequencing project, future aims are to ascertain whether certain of the novel variants could be used as biomarkers for early diagnosis and/or treatment decisions.
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Affiliation(s)
- Mikael Kronborg Christophersen
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Claus Høgdall
- The Juliane Marie Centre, Department of Gynaecology, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
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30
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Gusev A, Lawrenson K, Lin X, Lyra PC, Kar S, Vavra KC, Segato F, Fonseca MA, Lee JM, Pejovic T, Liu G, Karlan BY, Freedman ML, Noushmehr H, Monteiro AN, Pharoah PD, Pasaniuc B, Gayther SA. A transcriptome-wide association study of high-grade serous epithelial ovarian cancer identifies new susceptibility genes and splice variants. Nat Genet 2019; 51:815-823. [PMID: 31043753 PMCID: PMC6548545 DOI: 10.1038/s41588-019-0395-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/15/2019] [Indexed: 12/31/2022]
Abstract
We sought to identify susceptibility genes for high-grade serous ovarian cancer (HGSOC) by performing a transcriptome-wide association study of gene expression and splice junction usage in HGSOC-relevant tissue types (N = 2,169) and the largest genome-wide association study available for HGSOC (N = 13,037 cases and 40,941 controls). We identified 25 transcriptome-wide association study significant genes, 7 at the junction level only, including LRRC46 at 19q21.32, (P = 1 × 10-9), CHMP4C at 8q21 (P = 2 × 10-11) and a PRC1 junction at 15q26 (P = 7 × 10-9). In vitro assays for CHMP4C showed that the associated variant induces allele-specific exon inclusion (P = 0.0024). Functional screens in HGSOC cell lines found evidence of essentiality for three of the new genes we identified: HAUS6, KANSL1 and PRC1, with the latter comparable to MYC. Our study implicates at least one target gene for 6 out of 13 distinct genome-wide association study regions, identifying 23 new candidate susceptibility genes for HGSOC.
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Affiliation(s)
- Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kate Lawrenson
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xianzhi Lin
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Paulo C. Lyra
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Siddhartha Kar
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Kevin C. Vavra
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Felipe Segato
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Brazil
| | - Marcos A.S. Fonseca
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Janet M Lee
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tanya Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Gang Liu
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | | | - Beth Y. Karlan
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Houtan Noushmehr
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI, USA
| | - Alvaro N. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Paul D.P. Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Bogdan Pasaniuc
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Abstract
The IBDs, Crohn's disease and ulcerative colitis, are chronic inflammatory conditions of the gastrointestinal tract resulting from an aberrant immune response to enteric microbiota in genetically susceptible individuals. Disease presentation and progression within and across IBDs, especially Crohn's disease, are highly heterogeneous in location, severity of inflammation and other phenotypes. Current clinical classifications fail to accurately predict disease course and response to therapies. Genome-wide association studies have identified >240 loci that confer risk of IBD, but the clinical utility of these findings remains unclear, and mechanisms by which the genetic variants contribute to disease are largely unknown. In the past 5 years, the profiling of genome-wide gene expression, epigenomic features and gut microbiota composition in intestinal tissue and faecal samples has uncovered distinct molecular signatures that define IBD subtypes, including within Crohn's disease and ulcerative colitis. In this Review, we summarize studies in both adult and paediatric patients that have identified different IBD subtypes, which in some cases have been associated with distinct clinical phenotypes. We posit that genome-scale molecular phenotyping in large cohorts holds great promise not only to further our understanding of the diverse molecular causes of IBD but also for improving clinical trial design to develop more personalized disease management and treatment.
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Li B, Huang Q, Wei GH. The Role of HOX Transcription Factors in Cancer Predisposition and Progression. Cancers (Basel) 2019; 11:cancers11040528. [PMID: 31013831 PMCID: PMC6520925 DOI: 10.3390/cancers11040528] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022] Open
Abstract
Homeobox (HOX) transcription factors, encoded by a subset of homeodomain superfamily genes, play pivotal roles in many aspects of cellular physiology, embryonic development, and tissue homeostasis. Findings over the past decade have revealed that mutations in HOX genes can lead to increased cancer predisposition, and HOX genes might mediate the effect of many other cancer susceptibility factors by recognizing or executing altered genetic information. Remarkably, several lines of evidence highlight the interplays between HOX transcription factors and cancer risk loci discovered by genome-wide association studies, thereby gaining molecular and biological insight into cancer etiology. In addition, deregulated HOX gene expression impacts various aspects of cancer progression, including tumor angiogenesis, cell autophagy, proliferation, apoptosis, tumor cell migration, and metabolism. In this review, we will discuss the fundamental roles of HOX genes in cancer susceptibility and progression, highlighting multiple molecular mechanisms of HOX involved gene misregulation, as well as their potential implications in clinical practice.
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Affiliation(s)
- Bo Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China.
| | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China.
| | - Gong-Hong Wei
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, 90220 Oulu, Finland.
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eQTL analysis from co-localization of 2739 GWAS loci detects associated genes across 14 human cancers. J Theor Biol 2019; 462:240-246. [PMID: 30391648 DOI: 10.1016/j.jtbi.2018.10.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/28/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
Abstract
Genetic variants can predict other "linked" diseases because alterations in one or more genes in vivo may affect relevant phenotype properties. Our study systematically explored the pan-cancer common gene and cancer type-specific genes based on GWAS loci and TCGA data of multiple cancers. It was found that there were 17 SNPs were significantly associated with the expression of 18 genes. Associations between the 18 cis-regulatory genes and the pathologic stage of each cancer showed that MYL2 and PTGFR in HNSC, 4 genes (F8, SATB2, G6PD and UGT1A6) in KIRP, 3 genes (CHMP4C, MAP3K1 and MECP2) in LUAD were all strongly associated with cancer stage levels. Additionally, the survival association analysis showed that SATB2 was correlated with HNSC survival, and MPP1 was strongly associated with the survival of SARC. This study will shed light on the biological pathways involved in cancer-genetic associations, and has the potential to be applied to the predictions of the risk of cancers developing in healthy individuals.
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34
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Xiang Y, Ye Y, Zhang Z, Han L. Maximizing the Utility of Cancer Transcriptomic Data. Trends Cancer 2018; 4:823-837. [PMID: 30470304 DOI: 10.1016/j.trecan.2018.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/23/2018] [Accepted: 09/24/2018] [Indexed: 12/13/2022]
Abstract
Transcriptomic profiling has been applied to large numbers of cancer samples, by large-scale consortia, including The Cancer Genome Atlas, International Cancer Genome Consortium, and Cancer Cell Line Encyclopedia. Advances in mining cancer transcriptomic data enable us to understand the endless complexity of the cancer transcriptome and thereby to discover new biomarkers and therapeutic targets. In this paper, we review computational resources for deep mining of transcriptomic data to identify, quantify, and determine the functional effects and clinical utility of transcriptomic events, including noncoding RNAs, post-transcriptional regulation, exogenous RNAs, and transcribed genetic variants. These approaches can be applied to other complex diseases, thereby greatly leveraging the impact of this work.
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Affiliation(s)
- Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; These authors contributed equally
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; These authors contributed equally
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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Coan M, Rampioni Vinciguerra GL, Cesaratto L, Gardenal E, Bianchet R, Dassi E, Vecchione A, Baldassarre G, Spizzo R, Nicoloso MS. Exploring the Role of Fallopian Ciliated Cells in the Pathogenesis of High-Grade Serous Ovarian Cancer. Int J Mol Sci 2018; 19:ijms19092512. [PMID: 30149579 PMCID: PMC6163198 DOI: 10.3390/ijms19092512] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
High-grade serous epithelial ovarian cancer (HGSOC) is the fifth leading cause of cancer death in women and the first among gynecological malignancies. Despite an initial response to standard chemotherapy, most HGSOC patients relapse. To improve treatment options, we must continue investigating tumor biology. Tumor characteristics (e.g., risk factors and epidemiology) are valuable clues to accomplish this task. The two most frequent risk factors for HGSOC are the lifetime number of ovulations, which is associated with increased oxidative stress in the pelvic area caused by ovulation fluid, and a positive family history due to genetic factors. In the attempt to identify novel genetic factors (i.e., genes) associated with HGSOC, we observed that several genes in linkage with HGSOC are expressed in the ciliated cells of the fallopian tube. This finding made us hypothesize that ciliated cells, despite not being the cell of origin for HGSOC, may take part in HGSOC tumor initiation. Specifically, malfunction of the ciliary beat impairs the laminar fluid flow above the fallopian tube epithelia, thus likely reducing the clearance of oxidative stress caused by follicular fluid. Herein, we review the up-to-date findings dealing with HGSOC predisposition with the hypothesis that fallopian ciliated cells take part in HGSOC onset. Finally, we review the up-to-date literature concerning genes that are located in genomic loci associated with epithelial ovarian cancer (EOC) predisposition that are expressed by the fallopian ciliated cells.
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Affiliation(s)
- Michela Coan
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Gian Luca Rampioni Vinciguerra
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Laura Cesaratto
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Emanuela Gardenal
- Azienda Ospedaliera Universitaria Integrata, University of Verona, 37129 Verona, Italy.
| | - Riccardo Bianchet
- Scientific Direction, CRO Aviano Italy, Via Franco Gallini, 2 33081 Aviano, Italy.
| | - Erik Dassi
- Centre for Integrative Biology, University of Trento, 38122 Trento, Italy.
| | - Andrea Vecchione
- Department of clinical and molecular medicine, university of Rome "Sapienza", c/o sant andrea hospital, Via di Grottarossa 1035, 00189 Rome, Italy.
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Riccardo Spizzo
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
| | - Milena Sabrina Nicoloso
- Division of Molecular Oncology, Department of Translational Research, IRCCS CRO Aviano-National Cancer Institute, Via Franco Gallini, 2 33081 Aviano PN, Italy.
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36
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Zhou Y, Layton O, Hong L. Identification of Genes and Pathways Involved in Ovarian Epithelial Cancer by Bioinformatics Analysis. J Cancer 2018; 9:3016-3022. [PMID: 30210623 PMCID: PMC6134813 DOI: 10.7150/jca.26133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 06/09/2018] [Indexed: 01/05/2023] Open
Abstract
Ovarian epithelial cancer (OEC) is an often fatal disease with poor prognosis in women with high-stage disease. In contrast, ovarian low malignant potential (LMP) tumors with favorable prognosis behaves as a disease between benign and malignant tumors. The involved genes and pathways between benign-like LMP and aggressive OEC are largely unknown. This study integrated two cohorts profile datasets to investigate the potential key candidate genes and pathways associated with OEC. Gene expression in two datasets (GSE9891 and GSE12172), including 327 OECs and 48 LMP tumors, were analyzed. 559 differentially expressed genes were found to overlap, 251 up-regulated and 308 down-regulated. Subsequently, analysis of gene ontology, signaling pathway enrichment and protein-protein interaction (PPI) network was performed. Gene ontology analysis clustered the up-regulated and down-regulated genes based on significant enrichment. 282 nodes/ differentially expressed genes (DEGs) were identified from DEGs PPI network complex, and two most significant k-clique modules were identified from PPI. In a summary, using integrated bioinformatics analysis, we are able to identify biomarkers potentially significant in the pathogenesis of OEC, which can improve our understanding of the cause and molecular events. These candidate genes and pathways could be used for further confirmation, and lead to better disease diagnose and therapy.
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Affiliation(s)
- Yun Zhou
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, P.R. China
| | - Olivia Layton
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Li Hong
- Department of Gynaecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, P.R. China
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37
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Early transcriptional response of human ovarian and fallopian tube surface epithelial cells to norepinephrine. Sci Rep 2018; 8:8291. [PMID: 29844388 PMCID: PMC5974302 DOI: 10.1038/s41598-018-26670-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/17/2018] [Indexed: 01/14/2023] Open
Abstract
Evidence from human and animal studies suggests that chronic behavioral stress and resulting activation of the sympathetic nervous system may influence initiation and progression of tumors. However, the underlying mechanisms for these observations are poorly understood. The purpose of this study is to explore the effects of adrenergic signaling on cell line models derived from normal cells presumed to originate epithelial ovarian cancers. Here we explored the effects of the stress-related hormone, norepinephrine, on the transcriptional program of normal immortalized ovarian (iOSE) and fallopian tube (iFTSEC) surface epithelial cells. Analysis of RNA-Seq data of treated and untreated cells revealed a significant overlap between the responses in iOSE and iFTSEC cells. Most genes modulated by norepinephrine in ovarian and fallopian tube epithelial cells are already expressed in normal ovarian and fallopian tissue and cells. For several genes, expression changes were reflected at the protein level. Genes in immune-related and developmental pathways were enriched in the set of genes modulated by norepinephrine. We identified HOXA5, SPIB, REL, SRF, SP1, NFKB1, MEF2A, E2F1, and EGR1 transcription factor binding sites to be highly enriched in our dataset. These data represent the early transcriptional response to norepinephrine in cells postulated to originate epithelial ovarian cancer.
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38
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Kar SP, Berchuck A, Gayther SA, Goode EL, Moysich KB, Pearce CL, Ramus SJ, Schildkraut JM, Sellers TA, Pharoah PDP. Common Genetic Variation and Susceptibility to Ovarian Cancer: Current Insights and Future Directions. Cancer Epidemiol Biomarkers Prev 2018; 27:395-404. [PMID: 28615364 DOI: 10.1158/1055-9965.epi-17-0315] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/24/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022] Open
Abstract
In this review, we summarize current progress in the genetic epidemiology of epithelial ovarian cancer (EOC), focusing exclusively on elucidating the role of common germline genetic variation in conferring susceptibility to EOC. We provide an overview of the more than 30 EOC risk loci identified to date by genome-wide association studies (GWAS) and describe the contribution of large-scale, cross-cancer type, custom genotyping projects, such as the OncoArray and the Collaborative Oncological Gene-Environment Study, to locus discovery and replication. We discuss the histotype-specific nature of these EOC risk loci, pleiotropy, or overlapping genetic effects between EOC and other hormone-related cancer types, and the application of findings to polygenic risk prediction for EOC. The second part of the article offers a concise review of primarily laboratory-based studies that have led to the identification of several putative EOC susceptibility genes using common variants at the known EOC risk loci as starting points. More global biological insights emerging from network- and pathway-based analyses of GWAS for EOC susceptibility are also highlighted. Finally, we delve into potential future directions, including the need to identify EOC risk loci in non-European populations and the next generation of GWAS functional studies that are likely to involve genome editing to establish the cell type-specific carcinogenic effects of EOC risk variants Cancer Epidemiol Biomarkers Prev; 27(4); 395-404. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom.
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Simon A Gayther
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Susan J Ramus
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Virginia
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom.
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
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39
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Powell JE, Fung JN, Shakhbazov K, Sapkota Y, Cloonan N, Hemani G, Hillman KM, Kaufmann S, Luong HT, Bowdler L, Painter JN, Holdsworth-Carson SJ, Visscher PM, Dinger ME, Healey M, Nyholt DR, French JD, Edwards SL, Rogers PAW, Montgomery GW. Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339. Hum Mol Genet 2018; 25:5046-5058. [PMID: 28171565 DOI: 10.1093/hmg/ddw320] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/28/2016] [Accepted: 09/12/2016] [Indexed: 01/16/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified markers within the WNT4 region on chromosome 1p36.12 showing consistent and strong association with increasing endometriosis risk. Fine mapping using sequence and imputed genotype data has revealed strong candidates for the causal SNPs within these critical regions; however, the molecular pathogenesis of these SNPs is currently unknown. We used gene expression data collected from whole blood from 862 individuals and endometrial tissue from 136 individuals from independent populations of European descent to examine the mechanism underlying endometriosis susceptibility. Association mapping results from 7,090 individuals (2,594 cases and 4,496 controls) supported rs3820282 as the SNP with the strongest association for endometriosis risk (P = 1.84 × 10−5, OR = 1.244 (1.126-1.375)). SNP rs3820282 is a significant eQTL in whole blood decreasing expression of LINC00339 (also known as HSPC157) and increasing expression of CDC42 (P = 2.0 ×10−54 and 4.5x10−4 respectively). The largest effects were for two LINC00339 probes (P = 2.0 ×10−54; 1.0 × 10−34). The eQTL for LINC00339 was also observed in endometrial tissue (P = 2.4 ×10−8) with the same direction of effect for both whole blood and endometrial tissue. There was no evidence for eQTL effects for WNT4. Chromatin conformation capture provides evidence for risk SNPs interacting with the promoters of both LINC00339 and CDC4 and luciferase reporter assays suggest the risk SNP rs12038474 is located in a transcriptional silencer for CDC42 and the risk allele increases expression of CDC42. However, no effect of rs3820282 was observed in the LINC00339 expression in Ishikawa cells. Taken together, our results suggest that SNPs increasing endometriosis risk in this region act through CDC42, but further functional studies are required to rule out inverse regulation of both LINC00339 and CDC42.
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Affiliation(s)
- Joseph E Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia.,The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jenny N Fung
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Konstantin Shakhbazov
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia
| | - Yadav Sapkota
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicole Cloonan
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Gibran Hemani
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia.,MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK
| | - Kristine M Hillman
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Hien T Luong
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Lisa Bowdler
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jodie N Painter
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah J Holdsworth-Carson
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Peter M Visscher
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia
| | - Marcel E Dinger
- Garvan Medical Research Institute, Sydney, Australia,St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2052, Australia and
| | - Martin Healey
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Dale R Nyholt
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Juliet D French
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stacey L Edwards
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Peter A W Rogers
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Grant W Montgomery
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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40
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Jones MR, Kamara D, Karlan BY, Pharoah PDP, Gayther SA. Genetic epidemiology of ovarian cancer and prospects for polygenic risk prediction. Gynecol Oncol 2017; 147:705-713. [PMID: 29054568 DOI: 10.1016/j.ygyno.2017.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022]
Abstract
Epithelial ovarian cancer (EOC) is a heterogeneous disease with a major heritable component. The different histotypes of invasive disease - high grade serous, clear cell, endometrioid and mucinous - are associated with different underlying genetic susceptibility and epidemiological and lifestyle risk factors, all of which contribute to the different biology and clinical characteristics of each histotype. A combination of familial and population based sequencing studies, and genome wide association studies (GWAS) have identified a range of genetic susceptibility alleles for EOC comprising rare but highly penetrant genes (e.g. BRCA1, BRCA2) that are responsible for familial clustering of ovarian cancer cases; more moderate penetrance susceptibility genes (e.g. BRIP1, RAD51C/D, MSH6); and multiple common but low penetrance susceptibility alleles identified by GWAS. Identifying genetic risk alleles for ovarian cancer has had a significant impact on disease prevention strategies; for example it is now routine clinical practice for individuals with germline BRCA1 and BRCA2 mutations to undergo risk reducing salpingo-oophorectomy. Because ovarian cancers are commonly diagnosed at a late clinical stage when the prognosis is poor, the continued development of genetic risk prediction and prevention strategies will represent an important approach to reduce mortality due to ovarian cancer. Advances in genomics technologies that enable more high-throughput genetic testing, combined with research studies that identify additional EOC risk alleles will likely provide further opportunities to establish polygenic risk prediction approaches, based on combinations of rare high/moderate penetrance susceptibility genes and common, low penetrance susceptibility alleles. This article reviews the current literature describing the genetic and epidemiological components of ovarian cancer risk, and discusses both the opportunities and challenges in using this information for clinical risk prediction and prevention.
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Affiliation(s)
- Michelle R Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Daniella Kamara
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Paul D P Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, 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.
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Sud A, Kinnersley B, Houlston RS. Genome-wide association studies of cancer: current insights and future perspectives. Nat Rev Cancer 2017; 17:692-704. [PMID: 29026206 DOI: 10.1038/nrc.2017.82] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) provide an agnostic approach for investigating the genetic basis of complex diseases. In oncology, GWAS of nearly all common malignancies have been performed, and over 450 genetic variants associated with increased risks have been identified. As well as revealing novel pathways important in carcinogenesis, these studies have shown that common genetic variation contributes substantially to the heritable risk of many common cancers. The clinical application of GWAS is starting to provide opportunities for drug discovery and repositioning as well as for cancer prevention. However, deciphering the functional and biological basis of associations is challenging and is in part a barrier to fully unlocking the potential of GWAS.
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Affiliation(s)
- Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
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42
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Kar SP, Adler E, Tyrer J, Hazelett D, Anton-Culver H, Bandera EV, Beckmann MW, Berchuck A, Bogdanova N, Brinton L, Butzow R, Campbell I, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Dansonka-Mieszkowska A, Doherty JA, Dörk T, Dürst M, Eccles D, Fasching PA, Flanagan J, Gentry-Maharaj A, Glasspool R, Goode EL, Goodman MT, Gronwald J, Heitz F, Hildebrandt MAT, Høgdall E, Høgdall CK, Huntsman DG, Jensen A, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Lambrechts D, Levine DA, Li Q, Lissowska J, Lu KH, Lubiński J, Massuger LFAG, McGuire V, McNeish I, Menon U, Modugno F, Monteiro AN, Moysich KB, Ness RB, Nevanlinna H, Paul J, Pearce CL, Pejovic T, Permuth JB, Phelan C, Pike MC, Poole EM, Ramus SJ, Risch HA, Rossing MA, Salvesen HB, Schildkraut JM, Sellers TA, Sherman M, Siddiqui N, Sieh W, Song H, Southey M, Terry KL, Tworoger SS, Walsh C, Wentzensen N, Whittemore AS, Wu AH, Yang H, Zheng W, Ziogas A, Freedman ML, Gayther SA, Pharoah PDP, Lawrenson K. Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. Br J Cancer 2017; 116:524-535. [PMID: 28103614 PMCID: PMC5318969 DOI: 10.1038/bjc.2016.426] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 11/23/2016] [Accepted: 11/29/2016] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified 18 loci associated with serous ovarian cancer (SOC) susceptibility but the biological mechanisms driving these findings remain poorly characterised. Germline cancer risk loci may be enriched for target genes of transcription factors (TFs) critical to somatic tumorigenesis. METHODS All 615 TF-target sets from the Molecular Signatures Database were evaluated using gene set enrichment analysis (GSEA) and three GWAS for SOC risk: discovery (2196 cases/4396 controls), replication (7035 cases/21 693 controls; independent from discovery), and combined (9627 cases/30 845 controls; including additional individuals). RESULTS The PAX8-target gene set was ranked 1/615 in the discovery (PGSEA<0.001; FDR=0.21), 7/615 in the replication (PGSEA=0.004; FDR=0.37), and 1/615 in the combined (PGSEA<0.001; FDR=0.21) studies. Adding other genes reported to interact with PAX8 in the literature to the PAX8-target set and applying an alternative to GSEA, interval enrichment, further confirmed this association (P=0.006). Fifteen of the 157 genes from this expanded PAX8 pathway were near eight loci associated with SOC risk at P<10-5 (including six with P<5 × 10-8). The pathway was also associated with differential gene expression after shRNA-mediated silencing of PAX8 in HeyA8 (PGSEA=0.025) and IGROV1 (PGSEA=0.004) SOC cells and several PAX8 targets near SOC risk loci demonstrated in vitro transcriptomic perturbation. CONCLUSIONS Putative PAX8 target genes are enriched for common SOC risk variants. This finding from our agnostic evaluation is of particular interest given that PAX8 is well-established as a specific marker for the cell of origin of SOC.
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Affiliation(s)
- Siddhartha P Kar
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Emily Adler
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Jonathan Tyrer
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Dennis Hazelett
- Bioinformatics and Computational Biology Research Center, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, UCI Center for Cancer Genetics Research & Prevention, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Matthias W Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, Erlangen 91054, Germany
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Natalia Bogdanova
- Radiation Oncology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ralf Butzow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki 00100, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC 3002, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Karen Carty
- The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Jenny Chang-Claude
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg 69120, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Daniel W Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Jennifer Anne Doherty
- Department of Epidemiology, The Geisel School of Medicine—at Dartmouth, Hanover, NH 03756, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena-University Hospital-Friedrich Schiller University, Jena 07737, Germany
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton SO16 5YA, UK
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen Nuremberg, Universitaetsstrasse 21-23, Erlangen 91054, Germany
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - James Flanagan
- Department of Surgery & Cancer, Imperial College London, London SW7 2AZ, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | | | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MI 55905, USA
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-001, Poland
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/ Evang. Huyssens-Stiftung/ Knappschaft GmbH, Essen 45136, Germany
- Department of Gynecology and Gynecologic Oncology, Dr Horst Schmidt Kliniken Wiesbaden, Wiesbaden 65199, Germany
| | - Michelle A T Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Estrid Høgdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen 1165, Denmark
| | - Claus K Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - David G Huntsman
- British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, BC Cancer Agency and University of British Columbia, Vancouver, BC V5Z 1L3, Canada
- Departments of Pathology and Laboratory Medicine and Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
- Department of Molecular Oncology, BC Cancer Agency Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29435, USA
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen 6500 HB, The Netherlands
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen 2100, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jolanta Kupryjanczyk
- Department of Pathology, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven 3000, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven 3000, Belgium
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Medical College of Xiamen University, Xiamen 361102, China
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02-781, Poland
| | - Karen H Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jan Lubiński
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-001, Poland
| | - Leon F A G Massuger
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gynaecology, Nijmegen 6500 HB, The Netherlands
| | - Valerie McGuire
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Iain McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow G12 0YN, UK
| | - Usha Menon
- Department of Women's Cancer, Institute for Women's Health, University College London, London W1T 7DN, UK
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Alvaro N Monteiro
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, TX 77030, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki 00100, Finland
| | - James Paul
- The Beatson West of Scotland Cancer Centre, Glasgow G12 0YN, UK
| | - Celeste L Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tanja Pejovic
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer B Permuth
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Catherine Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Susan J Ramus
- Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98109, USA
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Horpital, Bergen 5058, Norway
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5058, Norway
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, NC 27710, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Mark Sherman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow G4 0SF, UK
| | - Weiva Sieh
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3002, Australia
| | - Kathryn L Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice S Whittemore
- Department of Health Research and Policy—Epidemiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center Medicine, Nashville, TN 37232, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Simon A Gayther
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge CB1 8RN, UK
| | - Kate Lawrenson
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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43
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Amos CI, Dennis J, Wang Z, Byun J, Schumacher FR, Gayther SA, Casey G, Hunter DJ, Sellers TA, Gruber SB, Dunning AM, Michailidou K, Fachal L, Doheny K, Spurdle AB, Li Y, Xiao X, Romm J, Pugh E, Coetzee GA, Hazelett DJ, Bojesen SE, Caga-Anan C, Haiman CA, Kamal A, Luccarini C, Tessier D, Vincent D, Bacot F, Van Den Berg DJ, Nelson S, Demetriades S, Goldgar DE, Couch FJ, Forman JL, Giles GG, Conti DV, Bickeböller H, Risch A, Waldenberger M, Brüske-Hohlfeld I, Hicks BD, Ling H, McGuffog L, Lee A, Kuchenbaecker K, Soucy P, Manz J, Cunningham JM, Butterbach K, Kote-Jarai Z, Kraft P, FitzGerald L, Lindström S, Adams M, McKay JD, Phelan CM, Benlloch S, Kelemen LE, Brennan P, Riggan M, O'Mara TA, Shen H, Shi Y, Thompson DJ, Goodman MT, Nielsen SF, Berchuck A, Laboissiere S, Schmit SL, Shelford T, Edlund CK, Taylor JA, Field JK, Park SK, Offit K, Thomassen M, Schmutzler R, Ottini L, Hung RJ, Marchini J, Amin Al Olama A, Peters U, Eeles RA, Seldin MF, Gillanders E, Seminara D, Antoniou AC, Pharoah PDP, Chenevix-Trench G, Chanock SJ, Simard J, Easton DF. The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers. Cancer Epidemiol Biomarkers Prev 2017; 26:126-135. [PMID: 27697780 PMCID: PMC5224974 DOI: 10.1158/1055-9965.epi-16-0106] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/30/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR.
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Affiliation(s)
- Christopher I Amos
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinyoung Byun
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon A Gayther
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - David J Hunter
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Thomas A Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Stephen B Gruber
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Kimberly Doheny
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yafang Li
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Xiangjun Xiao
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jane Romm
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | | | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlisse Caga-Anan
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christopher A Haiman
- The Center for Bioinformatics and Functional Genomics at Cedars Sinai Medical Center, Greater Los Angeles Area, Los Angeles, California
| | - Ahsan Kamal
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Tessier
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Daniel Vincent
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - François Bacot
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - David J Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Stefanie Nelson
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Stephen Demetriades
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | | | | | - Judith L Forman
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - David V Conti
- Division of Biostatistics, Department of Preventive Medicine, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Angela Risch
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg, Member of the German Center for Lung Research, Heidelberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Irene Brüske-Hohlfeld
- Helmholtz Zentrum München, Institut für Epidemiologie I, Neuherberg, Oberschleissheim, Germany
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Hua Ling
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Lesley McGuffog
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Andrew Lee
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Karoline Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Penny Soucy
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Judith Manz
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Katja Butterbach
- Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Peter Kraft
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Liesel FitzGerald
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Cancer, Genetics and Immunology, Menzies Institute for Medical Research, Hobart, Australia
| | - Sara Lindström
- Department of Epidemiology, Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Marcia Adams
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James D McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Catherine M Phelan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sara Benlloch
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Marjorie Riggan
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Tracy A O'Mara
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Sune F Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew Berchuck
- Department of Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Sylvie Laboissiere
- Génome Québec Innovation Centre, Montreal, Canada and McGill University, Montreal, Canada
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Tameka Shelford
- Center for Inherited Disease Research, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jack A Taylor
- Molecular and Genetic Epidemiology Group, National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - John K Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sue K Park
- College of Medicine, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Hospital, New York, New York
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Rita Schmutzler
- Zentrum Familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza, University of Rome, Rome, Italy
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | | | - Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California
- Department of Internal Medicine, University of California at Davis, Davis, California
| | - Elizabeth Gillanders
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, Canada
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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Ponsuksili S, Trakooljul N, Hadlich F, Haack F, Murani E, Wimmers K. Genetically regulated hepatic transcripts and pathways orchestrate haematological, biochemical and body composition traits. Sci Rep 2016; 6:39614. [PMID: 28000754 PMCID: PMC5175187 DOI: 10.1038/srep39614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/22/2016] [Indexed: 01/19/2023] Open
Abstract
The liver is the central metabolic organ and exhibits fundamental functions in haematological traits. Hepatic expression, haematological, plasma biochemical, and body composition traits were assessed in a porcine model (n = 297) to establish tissue-specific genetic variations that influence the function of immune-metabolism-correlated expression networks. At FDR (false discovery rate) <1%, more than 3,600 transcripts were jointly correlated (r = |0.22-0.48|) with the traits. Functional enrichment analysis demonstrated common links of metabolic and immune traits. To understand how immune and metabolic traits are affected via genetic regulation of gene expression, eQTLs were assessed. 20517 significant (FDR < 5%) eQTLs for 1401 transcripts were identified, among which 443 transcripts were associated with at least one of the examined traits and had cis-eQTL (such as ACO1 (6.52 × 10-7) and SOD1 (6.41 × 10-30). The present study establishes a comprehensive view of hepatic gene activity which links together metabolic and immune traits in a porcine model for medical research.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Unit 'Functional Genome Analysis', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Nares Trakooljul
- Research Unit 'Genomics', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Frieder Hadlich
- Research Unit 'Functional Genome Analysis', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Fiete Haack
- Research Unit 'Functional Genome Analysis', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Eduard Murani
- Research Unit 'Genomics', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Klaus Wimmers
- Research Unit 'Genomics', Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
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Permuth JB, Reid B, Earp M, Chen YA, Monteiro AN, Chen Z, Group AOCSS, Chenevix-Trench G, Fasching PA, Beckmann MW, Lambrechts D, Vanderstichele A, Niewenhuyse EV, Vergote I, Rossing MA, Doherty JA, Chang-Claude J, Moysich K, Odunsi K, Goodman MT, Shvetsov YB, Wilkens LR, Thompson PJ, Dörk T, Bogdanova N, Butzow R, Nevanlinna H, Pelttari L, Leminen A, Modugno F, Edwards RP, Ness RB, Kelley J, Heitz F, Karlan B, Lester J, Kjaer SK, Jensen A, Giles G, Hildebrandt M, Liang D, Lu KH, Wu X, Levine DA, Bisogna M, Berchuck A, Cramer DW, Terry KL, Tworoger SS, Poole EM, Bandera EV, Fridley B, Cunningham J, Winham SJ, Olson SH, Orlow I, Bjorge L, Kiemeney LA, Massuger L, Pejovic T, Moffitt M, Le N, Cook LS, Brooks-Wilson A, Kelemen LE, Gronwald J, Lubinski J, Wentzensen N, Brinton LA, Lissowska J, Yang H, Hogdall E, Hogdall C, Lundvall L, Pharoah PD, Song H, Campbell I, Eccles D, McNeish I, Whittemore A, McGuire V, Sieh W, Rothstein J, Phelan CM, Risch H, Narod S, McLaughlin J, Anton-Culver H, Ziogas A, Menon U, Gayther S, Ramus SJ, Gentry-Maharaj A, Pearce CL, Wu AH, Kupryjanczyk J, Dansonka-Mieszkowska A, Schildkraut JM, Cheng JQ, Goode EL, Sellers TA. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. Oncotarget 2016; 7:72381-72394. [PMID: 27911851 PMCID: PMC5340123 DOI: 10.18632/oncotarget.10546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/13/2016] [Indexed: 01/05/2023] Open
Abstract
RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleotide polymorphisms (SNPs) in ADAR genes modify EOC susceptibility, potentially by altering ovarian tissue gene expression. Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 controls, we evaluated the associations of 5,303 SNPs in ADAD1, ADAR, ADAR2, ADAR3, and SND1. Unconditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI), with adjustment for European ancestry. We conducted gene-level analyses using the Admixture Maximum Likelihood (AML) test and the Sequence-Kernel Association test for common and rare variants (SKAT-CR). Association analysis revealed top risk-associated SNP rs77027562 (OR (95% CI)= 1.39 (1.17-1.64), P=1.0x10-4) in ADAR3 and rs185455523 in SND1 (OR (95% CI)= 0.68 (0.56-0.83), P=2.0x10-4). When restricting to serous histology (n=6,500), the magnitude of association strengthened for rs185455523 (OR=0.60, P=1.0x10-4). Gene-level analyses revealed that variation in ADAR was associated (P<0.05) with EOC susceptibility, with PAML=0.022 and PSKAT-CR=0.020. Expression quantitative trait locus analysis in EOC tissue revealed significant associations (P<0.05) with ADAR expression for several SNPs in ADAR, including rs1127313 (G/A), a SNP in the 3' untranslated region. In summary, germline variation involving RNA editing genes may influence EOC susceptibility, warranting further investigation of inherited and acquired alterations affecting RNA editing.
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Affiliation(s)
| | - Brett Reid
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Madalene Earp
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Y. Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - AOCS Study Group
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Georgia Chenevix-Trench
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Peter A. Fasching
- David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center, Erlangen, Germany
| | - Matthias W. Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center, Erlangen, Germany
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Adriaan Vanderstichele
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Els Van Niewenhuyse
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecologic Oncology, Department of Obstetrics and Gynaecology and Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - 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
| | - Jennifer Anne Doherty
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NY, USA
| | - Jenny Chang-Claude
- German Cancer Research Center, Division of Cancer Epidemiology, Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oshin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yurii B. Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Lynne R. Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oshin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Bogdanova
- Radiaton Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Ralf Butzow
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Liisa Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute & University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Robert P. Edwards
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute & University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Roberta B. Ness
- The University of Texas School of Public Health, Houston, TX, USA
| | - Joseph Kelley
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
- Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Klinik Wiesbaden, Wiesbaden, Germany
| | - Beth Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - 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
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Graham Giles
- Cancer Epidemiology Centre, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, University of Melbourne, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia
| | - Michelle Hildebrandt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, USA
| | - Karen H. Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shelley S. Tworoger
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Brooke Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA
| | - Julie Cunningham
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Sara H. Olson
- Memorial Sloan Kettering Cancer Center, Department of Epidemiology and Biostatistics, New York, NY, USA
| | - Irene Orlow
- Memorial Sloan Kettering Cancer Center, Department of Epidemiology and Biostatistics, New York, NY, USA
| | - Line Bjorge
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Lambertus A. Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, Netherlands
| | - Leon Massuger
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Gynaecology, Nijmegen, The Netherlands
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Melissa Moffitt
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Nhu Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Linda E. Kelemen
- Department of Public Health Sciences, Medical University of South Carolina College of Medicine, Charleston, SC, USA
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, The Maria Sklodowska-Curie Memorial Cancer Center, Warsaw, Poland
| | - Hanna Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Estrid Hogdall
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Claus Hogdall
- The Juliane Marie Centre, Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | - Lene Lundvall
- The Juliane Marie Centre, Department of Obstetrics and Gynecology, Rigshospitalet, Copenhagen, Denmark
| | - Paul D.P. Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - Iain McNeish
- Institute of Cancer Sciences, Unversity of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, UK
| | - Alice Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Valerie McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Harvey Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Steven Narod
- Women's College Research Institute, University of Toronto, Toronto, ON, Canada
| | | | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, UCI School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Usha Menon
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Simon Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | | | - Celeste Leigh Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Epidemology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, the Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joellen M. Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC, USA
- Cancer Control and Population Sciences, Duke Cancer Institute, Durham, NC, USA
| | - Jin Q. Cheng
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Ellen L. Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Ovarian Cancer Association Consortium
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46
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Genomic approach to understand association between single nucleotide polymorphisms and risk of Korean serous ovarian cancer at stage IIIc. Mol Cell Toxicol 2016. [DOI: 10.1007/s13273-016-0004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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