1
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Wotton JM, Peterson E, Flenniken AM, Bains RS, Veeraragavan S, Bower LR, Bubier JA, Parisien M, Bezginov A, Haselimashhadi H, Mason J, Moore MA, Stewart ME, Clary DA, Delbarre DJ, Anderson LC, D'Souza A, Goodwin LO, Harrison ME, Huang Z, Mckay M, Qu D, Santos L, Srinivasan S, Urban R, Vukobradovic I, Ward CS, Willett AM, Braun RE, Brown SD, Dickinson ME, Heaney JD, Kumar V, Lloyd KK, Mallon AM, McKerlie C, Murray SA, Nutter LM, Parkinson H, Seavitt JR, Wells S, Samaco RC, Chesler EJ, Smedley D, Diatchenko L, Baumbauer KM, Young EE, Bonin RP, Mandillo S, White JK. Identifying genetic determinants of inflammatory pain in mice using a large-scale gene-targeted screen. Pain 2022; 163:1139-1157. [PMID: 35552317 PMCID: PMC9100450 DOI: 10.1097/j.pain.0000000000002481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 02/03/2023]
Abstract
ABSTRACT Identifying the genetic determinants of pain is a scientific imperative given the magnitude of the global health burden that pain causes. Here, we report a genetic screen for nociception, performed under the auspices of the International Mouse Phenotyping Consortium. A biased set of 110 single-gene knockout mouse strains was screened for 1 or more nociception and hypersensitivity assays, including chemical nociception (formalin) and mechanical and thermal nociception (von Frey filaments and Hargreaves tests, respectively), with or without an inflammatory agent (complete Freund's adjuvant). We identified 13 single-gene knockout strains with altered nocifensive behavior in 1 or more assays. All these novel mouse models are openly available to the scientific community to study gene function. Two of the 13 genes (Gria1 and Htr3a) have been previously reported with nociception-related phenotypes in genetically engineered mouse strains and represent useful benchmarking standards. One of the 13 genes (Cnrip1) is known from human studies to play a role in pain modulation and the knockout mouse reported herein can be used to explore this function further. The remaining 10 genes (Abhd13, Alg6, BC048562, Cgnl1, Cp, Mmp16, Oxa1l, Tecpr2, Trim14, and Trim2) reveal novel pathways involved in nociception and may provide new knowledge to better understand genetic mechanisms of inflammatory pain and to serve as models for therapeutic target validation and drug development.
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Affiliation(s)
| | - Emma Peterson
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Ann M. Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Rasneer S. Bains
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Surabi Veeraragavan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | - Lynette R. Bower
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
| | | | - Marc Parisien
- Department of Anesthesia, Faculty of Medicine, Faculty of Dentistry, McGill University, Genome Building, Montreal, QC, Canada
| | - Alexandr Bezginov
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | | | - Michelle E. Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Dave A. Clary
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
| | - Daniel J. Delbarre
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | | | - Abigail D'Souza
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | | | - Mark E. Harrison
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Ziyue Huang
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Matthew Mckay
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Dawei Qu
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Luis Santos
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Subhiksha Srinivasan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Rachel Urban
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Igor Vukobradovic
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Christopher S. Ward
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | | | | | - Steve D.M. Brown
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, United States
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - K.C. Kent Lloyd
- Mouse Biology Program, University of California-Davis, Davis, CA, United States
- Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, United States
| | - Ann-Marie Mallon
- Mammalian Genetics Unit, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Colin McKerlie
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Lauryl M.J. Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, United Kingdom
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Didcot, Oxfordshire, United Kingdom
| | - Rodney C. Samaco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| | | | - Damian Smedley
- William Harvey Research Institute, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Luda Diatchenko
- Department of Anesthesia, Faculty of Medicine, Faculty of Dentistry, McGill University, Genome Building, Montreal, QC, Canada
| | | | - Erin E. Young
- Anesthesiology, University of Kansas School of Medicine, KU Medical Center, Kansas City, KS, United States
| | - Robert P. Bonin
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Silvia Mandillo
- Institute of Biochemistry and Cell Biology-National Research Council, IBBC-CNR, Monterotondo (RM), Italy
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2
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Errington TM, Denis A, Allison AB, Araiza R, Aza-Blanc P, Bower LR, Campos J, Chu H, Denson S, Donham C, Harr K, Haven B, Iorns E, Kwok J, McDonald E, Pelech S, Perfito N, Pike A, Sampey D, Settles M, Scott DA, Sharma V, Tolentino T, Trinh A, Tsui R, Willis B, Wood J, Young L. Experiments from unfinished Registered Reports in the Reproducibility Project: Cancer Biology. eLife 2021; 10:73430. [PMID: 34874009 PMCID: PMC8651290 DOI: 10.7554/elife.73430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/14/2021] [Indexed: 12/16/2022] Open
Abstract
As part of the Reproducibility Project: Cancer Biology, we published Registered Reports that described how we intended to replicate selected experiments from 29 high-impact preclinical cancer biology papers published between 2010 and 2012. Replication experiments were completed and Replication Studies reporting the results were submitted for 18 papers, of which 17 were accepted and published by eLife with the rejected paper posted as a preprint. Here, we report the status and outcomes obtained for the remaining 11 papers. Four papers initiated experimental work but were stopped without any experimental outcomes. Two papers resulted in incomplete outcomes due to unanticipated challenges when conducting the experiments. For the remaining five papers only some of the experiments were completed with the other experiments incomplete due to mundane technical or unanticipated methodological challenges. The experiments from these papers, along with the other experiments attempted as part of the Reproducibility Project: Cancer Biology, provides evidence about the challenges of repeating preclinical cancer biology experiments and the replicability of the completed experiments.
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Affiliation(s)
| | | | - Anne B Allison
- Piedmont Virginia Community College, Charlottesville, United States
| | - Renee Araiza
- University of California, Davis, Davis, United States
| | | | | | | | - Heidi Chu
- Applied Biological Materials, Richmond, Canada
| | - Sarah Denson
- University of California, Davis, Davis, United States
| | | | - Kaitlyn Harr
- University of Virginia, Charlottesville, United States
| | | | | | - Jennie Kwok
- Applied Biological Materials, Richmond, Canada
| | - Elysia McDonald
- Drexel University College of Medicine, Philadelphia, United States
| | - Steven Pelech
- Kinexus Bioinformatics, Vancouver, Canada.,University of British Columbia, Vancouver, United States
| | | | - Amanda Pike
- Applied Biological Materials, Richmond, Canada
| | | | | | - David A Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | | | | | | | | | | | - Joshua Wood
- University of California, Davis, Davis, United States
| | - Lisa Young
- Applied Biological Materials, Richmond, Canada
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3
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Ding J, Ji J, Rabow Z, Shen T, Folz J, Brydges CR, Fan S, Lu X, Mehta S, Showalter MR, Zhang Y, Araiza R, Bower LR, Lloyd KCK, Fiehn O. A metabolome atlas of the aging mouse brain. Nat Commun 2021; 12:6021. [PMID: 34654818 PMCID: PMC8519999 DOI: 10.1038/s41467-021-26310-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
The mammalian brain relies on neurochemistry to fulfill its functions. Yet, the complexity of the brain metabolome and its changes during diseases or aging remain poorly understood. Here, we generate a metabolome atlas of the aging wildtype mouse brain from 10 anatomical regions spanning from adolescence to old age. We combine data from three assays and structurally annotate 1,547 metabolites. Almost all metabolites significantly differ between brain regions or age groups, but not by sex. A shift in sphingolipid patterns during aging related to myelin remodeling is accompanied by large changes in other metabolic pathways. Functionally related brain regions (brain stem, cerebrum and cerebellum) are also metabolically similar. In cerebrum, metabolic correlations markedly weaken between adolescence and adulthood, whereas at old age, cross-region correlation patterns reflect decreased brain segregation. We show that metabolic changes can be mapped to existing gene and protein brain atlases. The brain metabolome atlas is publicly available ( https://mouse.atlas.metabolomics.us/ ) and serves as a foundation dataset for future metabolomic studies.
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Affiliation(s)
- Jun Ding
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
- Department of Chemistry, Wuhan University, 430072, Wuhan, Hubei, P.R. China
| | - Jian Ji
- School of Food Science, State Key Laboratory of Food Science and Technology, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, 214122, Wuxi, Jiangsu, P.R. China
| | - Zachary Rabow
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Tong Shen
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Jacob Folz
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Christopher R Brydges
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Sili Fan
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Xinchen Lu
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Sajjan Mehta
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Megan R Showalter
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Ying Zhang
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Renee Araiza
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, 95618, USA
| | - Lynette R Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, 95618, USA
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California, Davis, Davis, CA, 95618, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA.
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4
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Rozman J, Rathkolb B, Oestereicher MA, Schütt C, Ravindranath AC, Leuchtenberger S, Sharma S, Kistler M, Willershäuser M, Brommage R, Meehan TF, Mason J, Haselimashhadi H, Hough T, Mallon AM, Wells S, Santos L, Lelliott CJ, White JK, Sorg T, Champy MF, Bower LR, Reynolds CL, Flenniken AM, Murray SA, Nutter LMJ, Svenson KL, West D, Tocchini-Valentini GP, Beaudet AL, Bosch F, Braun RB, Dobbie MS, Gao X, Herault Y, Moshiri A, Moore BA, Kent Lloyd KC, McKerlie C, Masuya H, Tanaka N, Flicek P, Parkinson HE, Sedlacek R, Seong JK, Wang CKL, Moore M, Brown SD, Tschöp MH, Wurst W, Klingenspor M, Wolf E, Beckers J, Machicao F, Peter A, Staiger H, Häring HU, Grallert H, Campillos M, Maier H, Fuchs H, Gailus-Durner V, Werner T, Hrabe de Angelis M. Identification of genetic elements in metabolism by high-throughput mouse phenotyping. Nat Commun 2018; 9:288. [PMID: 29348434 PMCID: PMC5773596 DOI: 10.1038/s41467-017-01995-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 10/30/2017] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome.
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Affiliation(s)
- Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, Feodor-Lynen Strasse 25, 81377, Munich, Germany
| | - Manuela A Oestereicher
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Aakash Chavan Ravindranath
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Sapna Sharma
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Kistler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Monja Willershäuser
- Chair of Molecular Nutritional Medicine, Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354, Freising, Germany
- EKFZ - Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tertius Hough
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Oxfordshire, OX11 0RD, UK
| | - Christopher J Lelliott
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 Rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Parc d'innovation, 1 Rue Laurent Fries - BP 10142, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Marie-France Champy
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 Rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Parc d'innovation, 1 Rue Laurent Fries - BP 10142, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Lynette R Bower
- Mouse Biology Program, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Corey L Reynolds
- Department of Molecular and Human Genetics, Baylor College of Medicine, 7702 Main St, Houston Medical Center, Houston, TX, 77030-4406, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, 25 Orde St, Toronto, M5T 3H7, ON, Canada
- The Hospital for Sick Children, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Stephen A Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, 25 Orde St, Toronto, M5T 3H7, ON, Canada
- The Hospital for Sick Children, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Karen L Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - David West
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via E. Ramarini 32, Monterotondo Scalo, RM, 00015, Italy
| | - Arthur L Beaudet
- The Centre for Phenogenomics, 25 Orde St, Toronto, M5T 3H7, ON, Canada
- The Hospital for Sick Children, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Fatima Bosch
- Center of Animal Biotechnology and Gene Therapy and Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Robert B Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Michael S Dobbie
- Australian Phenomics Network, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 Rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Parc d'innovation, 1 Rue Laurent Fries - BP 10142, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France
- Université de Strasbourg, 67404, Illkirch, France
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, 77 Cadillac Drive, Sacramento, 95825, CA, USA
| | - Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, U.C. Davis, One Shields Avenue, Davis, 95616, CA, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Colin McKerlie
- The Centre for Phenogenomics, 25 Orde St, Toronto, M5T 3H7, ON, Canada
- The Hospital for Sick Children, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Hiroshi Masuya
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Nobuhiko Tanaka
- RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen E Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Je Kyung Seong
- Korea Mouse Phenotyping Consortium (KMPC) and BK21 Program for Veterinary Science, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 599 Gwanangno, Gwanak-gu, Seoul, 151-742, South Korea
| | - Chi-Kuang Leo Wang
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), 128 Yen-Chiou-Yuan Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan
| | | | - Steve D Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Oxfordshire, OX11 0RD, UK
| | - Matthias H Tschöp
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
- Division of Metabolic Diseases, Department of Medicine, Technische Universität München, 80333, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Chair of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, Technical University of Munich, TUM School of Life Sciences Weihenstephan, 85354, Freising, Germany
- EKFZ - Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | - Eckhard Wolf
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Ludwig-Maximilians-Universität München, Gene Center, Institute of Molecular Animal Breeding and Biotechnology, Feodor-Lynen Strasse 25, 81377, Munich, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany
| | - Fausto Machicao
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076, Tübingen, Germany
| | - Andreas Peter
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076, Tübingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the Eberhard-Karls-University of Tuebingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany
| | - Harald Staiger
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the Eberhard-Karls-University of Tuebingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany
- Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls University Tübingen, 72076, Tübingen, Germany
| | - Hans-Ulrich Häring
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Department of Internal Medicine, Division of Endocrinology, Diabetology, Vascular Medicine, Nephrology and Clinical Chemistry, University of Tübingen, 72076, Tübingen, Germany
- Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Center Munich at the Eberhard-Karls-University of Tuebingen, Otfried-Müller-Str. 10, 72076, Tübingen, Germany
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Clinical Cooperation Group Type 2 Diabetes, Helmholtz Zentrum München and Ludwig-Maximilians Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Monica Campillos
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, 85354, Freising, Germany.
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5
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Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction. Nat Commun 2017; 8:886. [PMID: 29026089 PMCID: PMC5638796 DOI: 10.1038/s41467-017-00595-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 07/12/2017] [Indexed: 01/27/2023] Open
Abstract
The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function.The full extent of the genetic basis for hearing impairment is unknown. Here, as part of the International Mouse Phenotyping Consortium, the authors perform a hearing loss screen in 3006 mouse knockout strains and identify 52 new candidate genes for genetic hearing loss.
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Affiliation(s)
- Michael R Bowl
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle M Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Neil J Ingham
- King's College London, London, SE1 1UL, UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Greenaway
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sarah Taylor
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Natalja Kurbatova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Selina Pearson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Lynette R Bower
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - Dave A Clary
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - Hamid Meziane
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
| | - Patrick Reilly
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
| | - Osamu Minowa
- RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Lois Kelsey
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, I-00015, Monterotondo Scalo, Italy
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, 210061, Nanjing, China
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - William C Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark Moore
- IMPC, San Anselmo, California, 94960, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - John Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France
| | | | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | | | | | | | - David B West
- Childrens' Hospital Oakland Research Institute, Oakland, California, 94609, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqui White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen E Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Lydia M Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Karen P Steel
- King's College London, London, SE1 1UL, UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK.
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6
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Meehan TF, Conte N, West DB, Jacobsen JO, Mason J, Warren J, Chen CK, Tudose I, Relac M, Matthews P, Karp N, Santos L, Fiegel T, Ring N, Westerberg H, Greenaway S, Sneddon D, Morgan H, Codner GF, Stewart ME, Brown J, Horner N, Haendel M, Washington N, Mungall CJ, Reynolds CL, Gallegos J, Gailus-Durner V, Sorg T, Pavlovic G, Bower LR, Moore M, Morse I, Gao X, Tocchini-Valentini GP, Obata Y, Cho SY, Seong JK, Seavitt J, Beaudet AL, Dickinson ME, Herault Y, Wurst W, de Angelis MH, Lloyd KK, Flenniken AM, Nutter LMJ, Newbigging S, McKerlie C, Justice MJ, Murray SA, Svenson KL, Braun RE, White JK, Bradley A, Flicek P, Wells S, Skarnes WC, Adams DJ, Parkinson H, Mallon AM, Brown SD, Smedley D. Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. Nat Genet 2017; 49:1231-1238. [PMID: 28650483 PMCID: PMC5546242 DOI: 10.1038/ng.3901] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/25/2017] [Indexed: 12/12/2022]
Abstract
Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating a genome- and phenome-wide catalog of gene function by characterizing new knockout-mouse strains across diverse biological systems through a broad set of standardized phenotyping tests. All mice will be readily available to the biomedical community. Analyzing the first 3,328 genes identified models for 360 diseases, including the first models, to our knowledge, for type C Bernard-Soulier, Bardet-Biedl-5 and Gordon Holmes syndromes. 90% of our phenotype annotations were novel, providing functional evidence for 1,092 genes and candidates in genetically uncharacterized diseases including arrhythmogenic right ventricular dysplasia 3. Finally, we describe our role in variant functional validation with The 100,000 Genomes Project and others.
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Affiliation(s)
- Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nathalie Conte
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David B. West
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Julius O. Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Warren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chao-Kung Chen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ilinca Tudose
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mike Relac
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Matthews
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Luis Santos
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Tanja Fiegel
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Natalie Ring
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Simon Greenaway
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Duncan Sneddon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Hugh Morgan
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Gemma F Codner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Michelle E Stewart
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - James Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Neil Horner
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | | | - Melissa Haendel
- Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nicole Washington
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J. Mungall
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corey L Reynolds
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Valerie Gailus-Durner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Guillaume Pavlovic
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Lynette R Bower
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Mark Moore
- IMPC, San Anselmo, California 94960, USA
| | - Iva Morse
- Charles River Laboratories, Wilmington, Massachusetts 01887, USA
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Monterotondo Scalo I-00015, Italy
| | - Yuichi Obata
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Soo Young Cho
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- National Cancer Center, Goyang, Gyeonggi, 10408, Republic of Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, 08826, Republic of Korea
- Research Institute for Veterinary Science, Seoul National University, Republic of Korea
| | - John Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mary E. Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, F-67404 Illkirch-Graffenstaden, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
| | - Wolfgang Wurst
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - Martin Hrabe de Angelis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Neuherberg 85764, Germany
| | - K.C. Kent Lloyd
- Mouse Biology Program, University of California, Davis, California 95618, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | | | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario M5T 3H7, Canada
| | - Monica J. Justice
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | | | | | | | - Jacqueline K. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sara Wells
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - William C. Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Steve D.M. Brown
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire OX11 0RD, UK
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, E1 4NS, UK
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7
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Watkins WR, Spellicy RL, White KO, Sojka BZ, Bower LR. Water vapor absorption coefficients at HF laser wavelengths (2.64-2.93 microm). Appl Opt 1979; 18:1582-1589. [PMID: 20212897 DOI: 10.1364/ao.18.001582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Water vapor absorption coefficients are reported for nine HF laser wavelengths ranging from 3418.1600 cm(-1) to 3788.2253 cm(-1) for temperatures ranging from -18 degrees C to 25 degrees C. Pure water vapor as well as airbroadened (N(2)/O(2)) water vapor absorptions were measured at pressures from less than 1-764 Torr with some of the air-broadened data being used to extract effective self-to-foreign-broadening parameters in the vicinity of the laser frequencies. Limited data were also collected on O(2)-broadened water vapor absorption as well as pure and air-broadened CO(2) absorption. The CO(2) data agree reasonably well with theoretical predictions; but the air- and O(2)-broadened water vapor data show greater absorption than theoretically predicted and seem to imply a super Lorentz/Voigt line shape for H(2)O.
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8
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Watkins WR, White KO, Bower LR, Sojka BZ. Pressure dependence of the water vapor continuum absorption in the 3.5-4.0-microm region. Appl Opt 1979; 18:1149-1160. [PMID: 20208901 DOI: 10.1364/ao.18.001149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A line tunable deuterium fluoride laser was used to measure the pressure dependence of the water vapor continuum absorption at 25 degrees C in the 3.5-4.0-microm spectral region. From measurements of the absorption of 14.3 Torr of deuterium depleted water vapor buffered by several air-broadening pressures, an unexpectedly small foreign-to-self-broadening coefficient of 0.011 with a factor of 2 uncertainty as well as an unusually strong self-contribution for the water vapor continuum absorption were observed. These measurements can be used to infer contributions to the water vapor continuum in the 3-5-microm window from both far wing and aggregate-water-molecule type absorptions.
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