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Currall BB, Chen M, Sallari RC, Cotter M, Wong KE, Robertson NG, Penney KL, Lunardi A, Reschke M, Hickox AE, Yin Y, Wong GT, Fung J, Brown KK, Williamson RE, Sinnott-Armstrong NA, Kammin T, Ivanov A, Zepeda-Mendoza CJ, Shen J, Quade BJ, Signoretti S, Arnos KS, Banks AS, Patsopoulos N, Liberman MC, Kellis M, Pandolfi PP, Morton CC. Loss of LDAH associated with prostate cancer and hearing loss. Hum Mol Genet 2019; 27:4194-4203. [PMID: 30169630 DOI: 10.1093/hmg/ddy310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022] Open
Abstract
Great strides in gene discovery have been made using a multitude of methods to associate phenotypes with genetic variants, but there still remains a substantial gap between observed symptoms and identified genetic defects. Herein, we use the convergence of various genetic and genomic techniques to investigate the underpinnings of a constellation of phenotypes that include prostate cancer (PCa) and sensorineural hearing loss (SNHL) in a human subject. Through interrogation of the subject's de novo, germline, balanced chromosomal translocation, we first identify a correlation between his disorders and a poorly annotated gene known as lipid droplet associated hydrolase (LDAH). Using data repositories of both germline and somatic variants, we identify convergent genomic evidence that substantiates a correlation between loss of LDAH and PCa. This correlation is validated through both in vitro and in vivo models that show loss of LDAH results in increased risk of PCa and, to a lesser extent, SNHL. By leveraging convergent evidence in emerging genomic data, we hypothesize that loss of LDAH is involved in PCa and other phenotypes observed in support of a genotype-phenotype association in an n-of-one human subject.
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Affiliation(s)
- Benjamin B Currall
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Ming Chen
- Harvard Medical School, Boston, MA, USA.,Cancer Research Institute, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Richard C Sallari
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maura Cotter
- Center for Molecular Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Kristen E Wong
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Nahid G Robertson
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathryn L Penney
- Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrea Lunardi
- Harvard Medical School, Boston, MA, USA.,Cancer Research Institute, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Markus Reschke
- Harvard Medical School, Boston, MA, USA.,Cancer Research Institute, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ann E Hickox
- Harvard Medical School, Boston, MA, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Yanbo Yin
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA, USA.,Department of Otology and Laryngology, Harvard Medical School, Boston, MA, USA
| | - Garrett T Wong
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Fung
- Cancer Research Institute, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kerry K Brown
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Nicholas A Sinnott-Armstrong
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Andrew Ivanov
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Cinthya J Zepeda-Mendoza
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jun Shen
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA.,Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA
| | - Bradley J Quade
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sabina Signoretti
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen S Arnos
- Department of Science, Technology, & Mathematics, Gallaudet University, Washington, DC, USA
| | - Alexander S Banks
- Harvard Medical School, Boston, MA, USA.,Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Boston MA, USA
| | - Nikolaos Patsopoulos
- Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - M Charles Liberman
- Harvard Medical School, Boston, MA, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA, USA.,Department of Otology and Laryngology, Harvard Medical School, Boston, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pier Paolo Pandolfi
- Harvard Medical School, Boston, MA, USA.,Cancer Research Institute, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA.,Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
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