1
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Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
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Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
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2
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Roy TA, Bubier JA, Dickson PE, Wilcox TD, Ndukum J, Clark JW, Sukoff Rizzo SJ, Crabbe JC, Denegre JM, Svenson KL, Braun RE, Kumar V, Murray SA, White JK, Philip VM, Chesler EJ. Discovery and validation of genes driving drug-intake and related behavioral traits in mice. Genes Brain Behav 2024; 23:e12875. [PMID: 38164795 PMCID: PMC10780947 DOI: 10.1111/gbb.12875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/08/2023] [Accepted: 11/12/2023] [Indexed: 01/03/2024]
Abstract
Substance use disorders are heritable disorders characterized by compulsive drug use, the biological mechanisms for which remain largely unknown. Genetic correlations reveal that predisposing drug-naïve phenotypes, including anxiety, depression, novelty preference and sensation seeking, are predictive of drug-use phenotypes, thereby implicating shared genetic mechanisms. High-throughput behavioral screening in knockout (KO) mice allows efficient discovery of the function of genes. We used this strategy in two rounds of candidate prioritization in which we identified 33 drug-use candidate genes based upon predisposing drug-naïve phenotypes and ultimately validated the perturbation of 22 genes as causal drivers of substance intake. We selected 19/221 KO strains (8.5%) that had a difference from control on at least one drug-naïve predictive behavioral phenotype and determined that 15/19 (~80%) affected the consumption or preference for alcohol, methamphetamine or both. No mutant exhibited a difference in nicotine consumption or preference which was possibly confounded with saccharin. In the second round of prioritization, we employed a multivariate approach to identify outliers and performed validation using methamphetamine two-bottle choice and ethanol drinking-in-the-dark protocols. We identified 15/401 KO strains (3.7%, which included one gene from the first cohort) that differed most from controls for the predisposing phenotypes. 8 of 15 gene deletions (53%) affected intake or preference for alcohol, methamphetamine or both. Using multivariate and bioinformatic analyses, we observed multiple relations between predisposing behaviors and drug intake, revealing many distinct biobehavioral processes underlying these relationships. The set of mouse models identified in this study can be used to characterize these addiction-related processes further.
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Affiliation(s)
- Tyler A. Roy
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Jason A. Bubier
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Price E. Dickson
- Joan C Edwards School of MedicineMarshall UniversityHuntingtonWest VirginiaUSA
| | - Troy D. Wilcox
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Juliet Ndukum
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - James W. Clark
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Stacey J. Sukoff Rizzo
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - John C. Crabbe
- VA Portland Health Care SystemOregon Health & Science UniversityPortlandOregonUSA
| | - James M. Denegre
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Karen L. Svenson
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Robert E. Braun
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Vivek Kumar
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Stephen A. Murray
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | | | - Vivek M. Philip
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
| | - Elissa J. Chesler
- Center for Addiction BiologyThe Jackson LaboratoryBar HarborMaineUSA
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3
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Dumont BL, Gatti D, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Churchill G, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. bioRxiv 2023:2023.09.21.558738. [PMID: 37790321 PMCID: PMC10542534 DOI: 10.1101/2023.09.21.558738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.
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Affiliation(s)
- Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Daniel Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mallory A Ballinger
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Lin
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Taichi A Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA 85281
| | | | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Gary Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | | | - Michael W Nachman
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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4
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Roy TA, Bubier JA, Dickson PE, Wilcox TD, Ndukum J, Clark JW, Rizzo SJS, Crabbe JC, Denegre JM, Svenson KL, Braun RE, Kumar V, Murray SA, White JK, Philip VM, Chesler EJ. DISCOVERY AND VALIDATION OF GENES DRIVING DRUG-INTAKE AND RELATED BEHAVIORAL TRAITS IN MICE. bioRxiv 2023:2023.07.09.548280. [PMID: 37503148 PMCID: PMC10369854 DOI: 10.1101/2023.07.09.548280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Substance use disorders (SUDs) are heritable disorders characterized by compulsive drug use, but the biological mechanisms driving addiction remain largely unknown. Genetic correlations reveal that predisposing drug-naïve phenotypes, including anxiety, depression, novelty preference, and sensation seeking, are predictive of drug-use phenotypes, implicating shared genetic mechanisms. Because of this relationship, high-throughput behavioral screening of predictive phenotypes in knockout (KO) mice allows efficient discovery of genes likely to be involved in drug use. We used this strategy in two rounds of screening in which we identified 33 drug-use candidate genes and ultimately validated the perturbation of 22 of these genes as causal drivers of substance intake. In our initial round of screening, we employed the two-bottle-choice paradigms to assess alcohol, methamphetamine, and nicotine intake. We identified 19 KO strains that were extreme responders on at least one predictive phenotype. Thirteen of the 19 gene deletions (68%) significantly affected alcohol use three methamphetamine use, and two both. In the second round of screening, we employed a multivariate approach to identify outliers and performed validation using methamphetamine two-bottle choice and ethanol drinking-in-the-dark protocols. We identified 15 KO strains that were extreme responders across the predisposing drug-naïve phenotypes. Eight of the 15 gene deletions (53%) significantly affected intake or preference for three alcohol, eight methamphetamine or three both (3). We observed multiple relations between predisposing behaviors and drug intake, revealing many distinct biobehavioral processes underlying these relationships. The set of mouse models identified in this study can be used to characterize these addiction-related processes further.
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Affiliation(s)
| | | | - Price E. Dickson
- Joan C Edwards School of Medicine, Marshall University Huntington, WV
| | | | | | | | - Stacey J. Sukoff Rizzo
- The Jackson Laboratory, Bar Harbor, ME
- University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - John C. Crabbe
- Oregon Health & Science University and VA Portland Health Care System, Portland, OR
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5
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Peterson KA, Khalouei S, Hanafi N, Wood JA, Lanza DG, Lintott LG, Willis BJ, Seavitt JR, Braun RE, Dickinson ME, White JK, Lloyd KCK, Heaney JD, Murray SA, Ramani A, Nutter LMJ. Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity. Commun Biol 2023; 6:626. [PMID: 37301944 PMCID: PMC10257658 DOI: 10.1038/s42003-023-04974-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Genome editing with CRISPR-associated (Cas) proteins holds exceptional promise for "correcting" variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations.
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Affiliation(s)
| | - Sam Khalouei
- The Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Personalis, Inc. 1330 O'Brien Drive, Menlo Park, CA, USA
| | - Nour Hanafi
- The Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Joshua A Wood
- Mouse Biology Program, University of California Davis, California, CA, USA
- The Jackson Laboratory, Bar Harbor, Maine, ME, USA
| | - Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lauri G Lintott
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Brandon J Willis
- Mouse Biology Program, University of California Davis, California, CA, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Mary E Dickinson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | | | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, California, CA, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Arun Ramani
- The Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Invitae, San Francisco, CA, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, Canada.
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6
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Oestereicher MA, Wotton JM, Ayabe S, Bou About G, Cheng TK, Choi JH, Clary D, Dew EM, Elfertak L, Guimond A, Haseli Mashhadi H, Heaney JD, Kelsey L, Keskivali-Bond P, Lopez Gomez F, Marschall S, McFarland M, Meziane H, Munoz Fuentes V, Nam KH, Nichtová Z, Pimm D, Bower L, Prochazka J, Rozman J, Santos L, Stewart M, Tanaka N, Ward CS, Willett AME, Wilson R, Braun RE, Dickinson ME, Flenniken AM, Herault Y, Lloyd KCK, Mallon AM, McKerlie C, Murray SA, Nutter LMJ, Sedlacek R, Seong JK, Sorg T, Tamura M, Wells S, Schneltzer E, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, White JK, Spielmann N. Comprehensive ECG reference intervals in C57BL/6N substrains provide a generalizable guide for cardiac electrophysiology studies in mice. Mamm Genome 2023; 34:180-199. [PMID: 37294348 PMCID: PMC10290602 DOI: 10.1007/s00335-023-09995-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023]
Abstract
Reference ranges provide a powerful tool for diagnostic decision-making in clinical medicine and are enormously valuable for understanding normality in pre-clinical scientific research that uses in vivo models. As yet, there are no published reference ranges for electrocardiography (ECG) in the laboratory mouse. The first mouse-specific reference ranges for the assessment of electrical conduction are reported herein generated from an ECG dataset of unprecedented scale. International Mouse Phenotyping Consortium data from over 26,000 conscious or anesthetized C57BL/6N wildtype control mice were stratified by sex and age to develop robust ECG reference ranges. Interesting findings include that heart rate and key elements from the ECG waveform (RR-, PR-, ST-, QT-interval, QT corrected, and QRS complex) demonstrate minimal sexual dimorphism. As expected, anesthesia induces a decrease in heart rate and was shown for both inhalation (isoflurane) and injectable (tribromoethanol) anesthesia. In the absence of pharmacological, environmental, or genetic challenges, we did not observe major age-related ECG changes in C57BL/6N-inbred mice as the differences in the reference ranges of 12-week-old compared to 62-week-old mice were negligible. The generalizability of the C57BL/6N substrain reference ranges was demonstrated by comparison with ECG data from a wide range of non-IMPC studies. The close overlap in data from a wide range of mouse strains suggests that the C57BL/6N-based reference ranges can be used as a robust and comprehensive indicator of normality. We report a unique ECG reference resource of fundamental importance for any experimental study of cardiac function in mice.
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Affiliation(s)
- Manuela A Oestereicher
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Janine M Wotton
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Ghina Bou About
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Tsz Kwan Cheng
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Jae-Hoon Choi
- Department of Life Science, College of Natural Sciences, Hanyang Institute of Bioscience and Biotechnology, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Dave Clary
- Mouse Biology Program, University of California, 2795 Second Street Suite 400, Davis, CA, 95618, USA
| | - Emily M Dew
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Lahcen Elfertak
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Alain Guimond
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Jason D Heaney
- Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Lois Kelsey
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Piia Keskivali-Bond
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Federico Lopez Gomez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Susan Marschall
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Violeta Munoz Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Ki-Hoan Nam
- Korea Mouse Phenotyping Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Zuzana Nichtová
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dale Pimm
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Lynette Bower
- Mouse Biology Program, University of California, 2795 Second Street Suite 400, Davis, CA, 95618, USA
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Rozman
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Luis Santos
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Nobuhiko Tanaka
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Christopher S Ward
- Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | - Robert Wilson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Robert E Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mary E Dickinson
- Integrative Physiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, 2795 Second Street Suite 400, Davis, CA, 95618, USA
| | - Ann-Marie Mallon
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Stephen A Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, and Interdisciplinary Program for Bioinformatics, Korea Mouse Phenotyping CenterBK21 Plus Program for Advanced Veterinary Science, Research Institute for Veterinary ScienceSeoul National University, 599 Gwanak-Ro, Gwanak-Gu, Seoul, 08826, Republic of Korea
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut de La Clinique de La Souris, PHENOMIN, 1 Rue Laurent Fries, 67404, Illkirch, France
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Elida Schneltzer
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische 83 Universität München, Alte Akademie 8, 85354, Freising, Germany.
- German Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
| | | | - Nadine Spielmann
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
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7
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Murdy TJ, Dunn AR, Singh S, Telpoukhovskaia MA, Zhang S, White JK, Kahn I, Febo M, Kaczorowski CC. Leveraging genetic diversity in mice to inform individual differences in brain microstructure and memory. Front Behav Neurosci 2023; 16:1033975. [PMID: 36703722 PMCID: PMC9871587 DOI: 10.3389/fnbeh.2022.1033975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/08/2022] [Indexed: 01/11/2023] Open
Abstract
In human Alzheimer's disease (AD) patients and AD mouse models, both differential pre-disease brain features and differential disease-associated memory decline are observed, suggesting that certain neurological features may protect against AD-related cognitive decline. The combination of these features is known as brain reserve, and understanding the genetic underpinnings of brain reserve may advance AD treatment in genetically diverse human populations. One potential source of brain reserve is brain microstructure, which is genetically influenced and can be measured with diffusion MRI (dMRI). To investigate variation of dMRI metrics in pre-disease-onset, genetically diverse AD mouse models, we utilized a population of genetically distinct AD mice produced by crossing the 5XFAD transgenic mouse model of AD to 3 inbred strains (C57BL/6J, DBA/2J, FVB/NJ) and two wild-derived strains (CAST/EiJ, WSB/EiJ). At 3 months of age, these mice underwent diffusion magnetic resonance imaging (dMRI) to probe neural microanatomy in 83 regions of interest (ROIs). At 5 months of age, these mice underwent contextual fear conditioning (CFC). Strain had a significant effect on dMRI measures in most ROIs tested, while far fewer effects of sex, sex*strain interactions, or strain*sex*5XFAD genotype interactions were observed. A main effect of 5XFAD genotype was observed in only 1 ROI, suggesting that the 5XFAD transgene does not strongly disrupt neural development or microstructure of mice in early adulthood. Strain also explained the most variance in mouse baseline motor activity and long-term fear memory. Additionally, significant effects of sex and strain*sex interaction were observed on baseline motor activity, and significant strain*sex and sex*5XFAD genotype interactions were observed on long-term memory. We are the first to study the genetic influences of brain microanatomy in genetically diverse AD mice. Thus, we demonstrated that strain is the primary factor influencing brain microstructure in young adult AD mice and that neural development and early adult microstructure are not strongly altered by the 5XFAD transgene. We also demonstrated that strain, sex, and 5XFAD genotype interact to influence memory in genetically diverse adult mice. Our results support the usefulness of the 5XFAD mouse model and convey strong relationships between natural genetic variation, brain microstructure, and memory.
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Affiliation(s)
| | - Amy R. Dunn
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Surjeet Singh
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | | | | | - Itamar Kahn
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Marcelo Febo
- Department of Neuroscience, University of Florida College of Medicine, Gainesville, FL, United States
| | - Catherine C. Kaczorowski
- The Jackson Laboratory, Bar Harbor, ME, United States,*Correspondence: Catherine C. Kaczorowski,
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8
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Cacheiro P, Westerberg CH, Mager J, Dickinson ME, Nutter LMJ, Muñoz-Fuentes V, Hsu CW, Van den Veyver IB, Flenniken AM, McKerlie C, Murray SA, Teboul L, Heaney JD, Lloyd KCK, Lanoue L, Braun RE, White JK, Creighton AK, Laurin V, Guo R, Qu D, Wells S, Cleak J, Bunton-Stasyshyn R, Stewart M, Harrisson J, Mason J, Haseli Mashhadi H, Parkinson H, Mallon AM, Smedley D. Mendelian gene identification through mouse embryo viability screening. Genome Med 2022; 14:119. [PMID: 36229886 PMCID: PMC9563108 DOI: 10.1186/s13073-022-01118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND The diagnostic rate of Mendelian disorders in sequencing studies continues to increase, along with the pace of novel disease gene discovery. However, variant interpretation in novel genes not currently associated with disease is particularly challenging and strategies combining gene functional evidence with approaches that evaluate the phenotypic similarities between patients and model organisms have proven successful. A full spectrum of intolerance to loss-of-function variation has been previously described, providing evidence that gene essentiality should not be considered as a simple and fixed binary property. METHODS Here we further dissected this spectrum by assessing the embryonic stage at which homozygous loss-of-function results in lethality in mice from the International Mouse Phenotyping Consortium, classifying the set of lethal genes into one of three windows of lethality: early, mid, or late gestation lethal. We studied the correlation between these windows of lethality and various gene features including expression across development, paralogy and constraint metrics together with human disease phenotypes. We explored a gene similarity approach for novel gene discovery and investigated unsolved cases from the 100,000 Genomes Project. RESULTS We found that genes in the early gestation lethal category have distinct characteristics and are enriched for genes linked with recessive forms of inherited metabolic disease. We identified several genes sharing multiple features with known biallelic forms of inborn errors of the metabolism and found signs of enrichment of biallelic predicted pathogenic variants among early gestation lethal genes in patients recruited under this disease category. We highlight two novel gene candidates with phenotypic overlap between the patients and the mouse knockouts. CONCLUSIONS Information on the developmental period at which embryonic lethality occurs in the knockout mouse may be used for novel disease gene discovery that helps to prioritise variants in unsolved rare disease cases.
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Affiliation(s)
- Pilar Cacheiro
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lauryl M J Nutter
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA.,Department of Education, Innovation and Technology, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Ann M Flenniken
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Colin McKerlie
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | | | | | - Amie K Creighton
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Valerie Laurin
- The Hospital for Sick Children, The Centre for Phenogenomics, Toronto, Canada
| | - Ruolin Guo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Dawei Qu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, The Centre for Phenogenomics, Toronto, Canada
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - James Cleak
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | | | - Michelle Stewart
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jackie Harrisson
- The Mary Lyon Centre, MRC Harwell Institute, Harwell, Oxfordshire, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Hamed Haseli Mashhadi
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, UK.
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9
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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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10
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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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11
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Geyer SH, Maurer-Gesek B, Reissig LF, Rose J, Prin F, Wilson R, Galli A, Tudor C, White JK, Mohun TJ, Weninger WJ. The venous system of E14.5 mouse embryos-reference data and examples for diagnosing malformations in embryos with gene deletions. J Anat 2021; 240:11-22. [PMID: 34435363 PMCID: PMC8655187 DOI: 10.1111/joa.13536] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/23/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/29/2022] Open
Abstract
Approximately one‐third of randomly produced knockout mouse lines produce homozygous offspring, which fail to survive the perinatal period. The majority of these die around or after embryonic day (E)14.5, presumably from cardiovascular insufficiency. For diagnosing structural abnormalities underlying death and diseases and for researching gene function, the phenotype of these individuals has to be analysed. This makes the creation of reference data, which define normal anatomy and normal variations the highest priority. While such data do exist for the heart and arteries, they are still missing for the venous system. Here we provide high‐quality descriptive and metric information on the normal anatomy of the venous system of E14.5 embryos. Using high‐resolution digital volume data and 3D models from 206 genetically normal embryos, bred on the C57BL/6N background, we present precise descriptive and metric information of the venous system as it presents itself in each of the six developmental stages of E14.5. The resulting data shed new light on the maturation and remodelling of the venous system at transition of embryo to foetal life and provide a reference that can be used for detecting venous abnormalities in mutants. To explore this capacity, we analysed the venous phenotype of embryos from 7 knockout lines (Atp11a, Morc2a, 1700067K01Rik, B9d2, Oaz1, Celf4 and Coro1c). Careful comparisons enabled the diagnosis of not only simple malformations, such as dual inferior vena cava, but also complex and subtle abnormalities, which would have escaped diagnosis in the absence of detailed, stage‐specific referenced data.
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Affiliation(s)
- Stefan H Geyer
- Division of Anatomy, MIC, BioImaging Austria/CMI, Medical University of Vienna, Vienna, Austria
| | - Barbara Maurer-Gesek
- Division of Anatomy, MIC, BioImaging Austria/CMI, Medical University of Vienna, Vienna, Austria
| | - Lukas F Reissig
- Division of Anatomy, MIC, BioImaging Austria/CMI, Medical University of Vienna, Vienna, Austria
| | - Julia Rose
- Division of Anatomy, MIC, BioImaging Austria/CMI, Medical University of Vienna, Vienna, Austria
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Antonella Galli
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Catherine Tudor
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | - Wolfgang J Weninger
- Division of Anatomy, MIC, BioImaging Austria/CMI, Medical University of Vienna, Vienna, Austria
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12
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Butterfield NC, Curry KF, Steinberg J, Dewhurst H, Komla-Ebri D, Mannan NS, Adoum AT, Leitch VD, Logan JG, Waung JA, Ghirardello E, Southam L, Youlten SE, Wilkinson JM, McAninch EA, Vancollie VE, Kussy F, White JK, Lelliott CJ, Adams DJ, Jacques R, Bianco AC, Boyde A, Zeggini E, Croucher PI, Williams GR, Bassett JHD. Publisher Correction: Accelerating functional gene discovery in osteoarthritis. Nat Commun 2021; 12:3302. [PMID: 34050183 PMCID: PMC8163861 DOI: 10.1038/s41467-021-23768-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Katherine F Curry
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Julia Steinberg
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Cancer Council NSW, Sydney, NSW, 2000, Australia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Davide Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Naila S Mannan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Anne-Tounsia Adoum
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Julian A Waung
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Elena Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Scott E Youlten
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, NSW, 2010, Australia
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
- Centre for Integrated Research into Musculoskeletal Ageing and Sheffield Healthy Lifespan Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Elizabeth A McAninch
- Division of Endocrinology and Metabolism, Rush University Medical Center, Chicago, IL, 60612, USA
| | | | - Fiona Kussy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Jacques
- School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, S1 4DA, UK
| | - Antonio C Bianco
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Alan Boyde
- Dental Physical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Peter I Croucher
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, NSW, 2010, Australia
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK.
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK.
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13
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Butterfield NC, Curry KF, Steinberg J, Dewhurst H, Komla-Ebri D, Mannan NS, Adoum AT, Leitch VD, Logan JG, Waung JA, Ghirardello E, Southam L, Youlten SE, Wilkinson JM, McAninch EA, Vancollie VE, Kussy F, White JK, Lelliott CJ, Adams DJ, Jacques R, Bianco AC, Boyde A, Zeggini E, Croucher PI, Williams GR, Bassett JHD. Accelerating functional gene discovery in osteoarthritis. Nat Commun 2021; 12:467. [PMID: 33473114 PMCID: PMC7817695 DOI: 10.1038/s41467-020-20761-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 11/29/2019] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
Osteoarthritis causes debilitating pain and disability, resulting in a considerable socioeconomic burden, yet no drugs are available that prevent disease onset or progression. Here, we develop, validate and use rapid-throughput imaging techniques to identify abnormal joint phenotypes in randomly selected mutant mice generated by the International Knockout Mouse Consortium. We identify 14 genes with functional involvement in osteoarthritis pathogenesis, including the homeobox gene Pitx1, and functionally characterize 6 candidate human osteoarthritis genes in mouse models. We demonstrate sensitivity of the methods by identifying age-related degenerative joint damage in wild-type mice. Finally, we phenotype previously generated mutant mice with an osteoarthritis-associated polymorphism in the Dio2 gene by CRISPR/Cas9 genome editing and demonstrate a protective role in disease onset with public health implications. We hope this expanding resource of mutant mice will accelerate functional gene discovery in osteoarthritis and offer drug discovery opportunities for this common, incapacitating chronic disease.
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Affiliation(s)
- Natalie C Butterfield
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Katherine F Curry
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Julia Steinberg
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Cancer Council NSW, Sydney, NSW, 2000, Australia
| | - Hannah Dewhurst
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Davide Komla-Ebri
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Naila S Mannan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Anne-Tounsia Adoum
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Victoria D Leitch
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - John G Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Julian A Waung
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Elena Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK
| | - Lorraine Southam
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Scott E Youlten
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, NSW, 2010, Australia
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
- Centre for Integrated Research into Musculoskeletal Ageing and Sheffield Healthy Lifespan Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Elizabeth A McAninch
- Division of Endocrinology and Metabolism, Rush University Medical Center, Chicago, IL, 60612, USA
| | | | - Fiona Kussy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Jacques
- School of Health and Related Research (ScHARR), University of Sheffield, Sheffield, S1 4DA, UK
| | - Antonio C Bianco
- Section of Adult and Pediatric Endocrinology, Diabetes & Metabolism, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Alan Boyde
- Dental Physical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Eleftheria Zeggini
- Institute of Translational Genomics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Peter I Croucher
- The Garvan Institute of Medical Research and St. Vincent's Clinical School, University of New South Wales Medicine, Sydney, NSW, 2010, Australia
| | - Graham R Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK.
| | - J H Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, W12 0NN, UK.
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14
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Swan AL, Schütt C, Rozman J, del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density. PLoS Genet 2020; 16:e1009190. [PMID: 33370286 PMCID: PMC7822523 DOI: 10.1371/journal.pgen.1009190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/25/2020] [Revised: 01/22/2021] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease. Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.
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Affiliation(s)
- Anna L. Swan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | | | - Stefan Brandmaier
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Piia Keskivali-Bond
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raffaele Teperino
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ala Moshiri
- University of California-Davis School of Medicine, Sacramento, California, United States of America
| | - John R. Seavitt
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Derek D. Cissell
- Department of Surgical & Radiological Sciences, University of California, Davis, California, United States of America
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elif F. Acar
- The Center for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ann M. Flenniken
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Abdel Ayadi
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Heather Cater
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Juan Gallegos
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Elena J. Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Jason D. Heaney
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Sylvie Jacquot
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Connor Lally
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - John G. Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Lydia Teboul
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Colin McKerlie
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Lauryl M. J. Nutter
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristian F. Odfalk
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Corey L. Reynolds
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Frantisek Spoutil
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Karen L. Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Taylor S. Vales
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Sara E. Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine and Mouse Biology Program, University of California Davis
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- * E-mail:
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15
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Wotton JM, Peterson E, Anderson L, Murray SA, Braun RE, Chesler EJ, White JK, Kumar V. Machine learning-based automated phenotyping of inflammatory nocifensive behavior in mice. Mol Pain 2020; 16:1744806920958596. [PMID: 32955381 PMCID: PMC7509709 DOI: 10.1177/1744806920958596] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Indexed: 11/21/2022] Open
Abstract
The discovery and development of new and potentially nonaddictive pain therapeutics requires rapid, yet clinically relevant assays of nociception in preclinical models. A reliable and scalable automated scoring system for nocifensive behavior of mice in the formalin assay would dramatically lower the time and labor costs associated with experiments and reduce experimental variability. Here, we present a method that exploits machine learning techniques for video recordings that consists of three components: key point detection, per frame feature extraction using these key points, and classification of behavior using the GentleBoost algorithm. This approach to automation is flexible as different model classifiers or key points can be used with only small losses in accuracy. The adopted system identified the behavior of licking/biting of the hind paw with an accuracy that was comparable to a human observer (98% agreement) over 111 different short videos (total 284 min) at a resolution of 1 s. To test the system over longer experimental conditions, the responses of two inbred strains, C57BL/6NJ and C57BL/6J, were recorded over 90 min post formalin challenge. The automated system easily scored over 80 h of video and revealed strain differences in both response timing and amplitude. This machine learning scoring system provides the required accuracy, consistency, and ease of use that could make the formalin assay a feasible choice for large-scale genetic studies.
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16
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Racine JJ, Chapman HD, Doty R, Cairns BM, Hines TJ, Tadenev ALD, Anderson LC, Green T, Dyer ME, Wotton JM, Bichler Z, White JK, Ettinger R, Burgess RW, Serreze DV. T Cells from NOD- PerIg Mice Target Both Pancreatic and Neuronal Tissue. J Immunol 2020; 205:2026-2038. [PMID: 32938729 DOI: 10.4049/jimmunol.2000114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/13/2020] [Indexed: 11/19/2022]
Abstract
It has become increasingly appreciated that autoimmune responses against neuronal components play an important role in type 1 diabetes (T1D) pathogenesis. In fact, a large proportion of islet-infiltrating B lymphocytes in the NOD mouse model of T1D produce Abs directed against the neuronal type III intermediate filament protein peripherin. NOD-PerIg mice are a previously developed BCR-transgenic model in which virtually all B lymphocytes express the H and L chain Ig molecules from the intra-islet-derived anti-peripherin-reactive hybridoma H280. NOD-PerIg mice have accelerated T1D development, and PerIg B lymphocytes actively proliferate within islets and expand cognitively interactive pathogenic T cells from a pool of naive precursors. We now report adoptively transferred T cells or whole splenocytes from NOD-PerIg mice expectedly induce T1D in NOD.scid recipients but, depending on the kinetics of disease development, can also elicit a peripheral neuritis (with secondary myositis). This neuritis was predominantly composed of CD4+ and CD8+ T cells. Ab depletion studies showed neuritis still developed in the absence of NOD-PerIg CD8+ T cells but required CD4+ T cells. Surprisingly, sciatic nerve-infiltrating CD4+ cells had an expansion of IFN-γ- and TNF-α- double-negative cells compared with those within both islets and spleen. Nerve and islet-infiltrating CD4+ T cells also differed by expression patterns of CD95, PD-1, and Tim-3. Further studies found transitory early B lymphocyte depletion delayed T1D onset in a portion of NOD-PerIg mice, allowing them to survive long enough to develop neuritis outside of the transfer setting. Together, this study presents a new model of peripherin-reactive B lymphocyte-dependent autoimmune neuritis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zoë Bichler
- The Jackson Laboratory, Bar Harbor, ME 04609
| | | | - Rachel Ettinger
- Viela Bio, Gaithersburg, MD 20878; and.,Respiratory, Inflammation, and Autoimmunity, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878
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17
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Herbert E, Stewart M, Hutchison M, Flenniken AM, Qu D, Nutter LMJ, McKerlie C, Hobson L, Kick B, Lyons B, Wiegand JP, Doty R, Aguilar-Pimentel JA, Hrabe de Angelis M, Dickinson M, Seavitt J, White JK, Scudamore CL, Wells S. The occurrence of tarsal injuries in male mice of C57BL/6N substrains in multiple international mouse facilities. PLoS One 2020; 15:e0230162. [PMID: 32542000 PMCID: PMC7295225 DOI: 10.1371/journal.pone.0230162] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 11/19/2022] Open
Abstract
Dislocation in hindlimb tarsals are being observed at a low, but persistent frequency in group-housed adult male mice from C57BL/6N substrains. Clinical signs included a sudden onset of mild to severe unilateral or bilateral tarsal abduction, swelling, abnormal hindlimb morphology and lameness. Contraction of digits and gait abnormalities were noted in multiple cases. Radiographical and histological examination revealed caudal dislocation of the calcaneus and partial dislocation of the calcaneoquartal (calcaneus-tarsal bone IV) joint. The detection, frequency, and cause of this pathology in five large mouse production and phenotyping centres (MRC Harwell, UK; The Jackson Laboratory, USA; The Centre for Phenogenomics, Canada; German Mouse Clinic, Germany; Baylor College of Medicine, USA) are discussed.
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Affiliation(s)
- Eleanor Herbert
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire, United Kingdom
| | - Michelle Stewart
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Marie Hutchison
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Dawei Qu
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Liane Hobson
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Brenda Kick
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Bonnie Lyons
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Rosalinda Doty
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mary Dickinson
- Baylor College of Medicine, Houston, Texas, United States of America
| | - John Seavitt
- Baylor College of Medicine, Houston, Texas, United States of America
| | | | | | - Sara Wells
- Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, United Kingdom
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18
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Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao GX, Chan A, Ballesteros Reviriego C, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd CM, Cornall RJ, Maloy KJ, Grencis RK, Griffiths GM, Adams DJ, Hayday AC. High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Nat Immunol 2020; 21:86-100. [PMID: 31844327 PMCID: PMC7338221 DOI: 10.1038/s41590-019-0549-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/29/2019] [Indexed: 01/28/2023]
Abstract
By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic 'hits', of which most had no previous immunologic association. Furthermore, hits were collectively enriched in genes for which humans show poor tolerance to loss of function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with each other and with specific physiologic traits. Such linkages limit freedom of movement for individual immune parameters, thereby imposing genetically regulated 'immunologic structures', the integrity of which was associated with immunocompetence. Hence, we provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.
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Affiliation(s)
| | - Adam G Laing
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Anna Lorenc
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Dmitry S Ushakov
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | | | | | | | | | | | - Namita Saran
- Department of Immunobiology, King's College London, London, UK
| | | | - Belén Morón
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jua Iwasaki
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Philippa R Barton
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Susana Caetano
- Department of Immunobiology, King's College London, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Keng I Hng
- Department of Immunobiology, King's College London, London, UK
| | | | - Simon Forman
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | | | | | | | | | | | - Kolawole O Babalola
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jonathan Warren
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jeremy C Mason
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Amrutha Meeniga
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Natasha A Karp
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | - Brian Weinrick
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Albina Rahim
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Meskas
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Alice Yue
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Markus Lux
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Anna Chan
- Department of Immunobiology, King's College London, London, UK
| | | | | | | | | | - Matthew Edmans
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | | | - Markus Pasztorek
- Department of Immunobiology, King's College London, London, UK
- Department of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Terrence F Meehan
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ryan Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | | | - William Jacobs
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kevin J Maloy
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gillian M Griffiths
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | | | - Adrian C Hayday
- Department of Immunobiology, King's College London, London, UK.
- The Francis Crick Institute, London, UK.
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19
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Reissig LF, Herdina AN, Rose J, Maurer-Gesek B, Lane JL, Prin F, Wilson R, Hardman E, Galli A, Tudor C, Tuck E, Icoresi-Mazzeo C, White JK, Ryder E, Gleeson D, Adams DJ, Geyer SH, Mohun TJ, Weninger WJ. The Col4a2em1(IMPC)Wtsi mouse line: lessons from the Deciphering the Mechanisms of Developmental Disorders program. Biol Open 2019; 8:bio.042895. [PMID: 31331924 PMCID: PMC6737985 DOI: 10.1242/bio.042895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders (DMDD) program uses a systematic and standardised approach to characterise the phenotype of embryos stemming from mouse lines, which produce embryonically lethal offspring. Our study aims to provide detailed phenotype descriptions of homozygous Col4a2em1(IMPC)Wtsi mutants produced in DMDD and harvested at embryonic day 14.5. This shall provide new information on the role Col4a2 plays in organogenesis and demonstrate the capacity of the DMDD database for identifying models for researching inherited disorders. The DMDD Col4a2em1(IMPC)Wtsi mutants survived organogenesis and thus revealed the full spectrum of organs and tissues, the development of which depends on Col4a2 encoded proteins. They showed defects in the brain, cranial nerves, visual system, lungs, endocrine glands, skeleton, subepithelial tissues and mild to severe cardiovascular malformations. Together, this makes the DMDD Col4a2em1(IMPC)Wtsi line a useful model for identifying the spectrum of defects and for researching the mechanisms underlying autosomal dominant porencephaly 2 (OMIM # 614483), a rare human disease. Thus we demonstrate the general capacity of the DMDD approach and webpage as a valuable source for identifying mouse models for rare diseases. Summary: We define the spectrum of phenotypic abnormalities linked with Col4a2 disruption and demonstrate the opportunities the Deciphering the Mechanisms of Developmental Disorders (DMDD) program offers for exploring rare human diseases.
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Affiliation(s)
- Lukas F Reissig
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
| | - Anna Nele Herdina
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
| | - Julia Rose
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
| | - Barbara Maurer-Gesek
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
| | - Jenna L Lane
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Fabrice Prin
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robert Wilson
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emily Hardman
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Elizabeth Tuck
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Ed Ryder
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Diane Gleeson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
| | - Timothy J Mohun
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringer Str. 13, 1090 Vienna, Austria
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20
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Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Common and distinct transcriptional signatures of mammalian embryonic lethality. Nat Commun 2019; 10:2792. [PMID: 31243271 PMCID: PMC6594971 DOI: 10.1038/s41467-019-10642-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.
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Affiliation(s)
- John E Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Richard J White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicole Staudt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ian Packham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cecilia Mazzeo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Green
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Irene Papatheodoru
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Antonella Galli
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Myriam Hemberger
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Derek L Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Camena Bioscience, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Elizabeth Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - James C Smith
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Timothy Mohun
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
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21
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Ingham NJ, Pearson SA, Vancollie VE, Rook V, Lewis MA, Chen J, Buniello A, Martelletti E, Preite L, Lam CC, Weiss FD, Powis Z, Suwannarat P, Lelliott CJ, Dawson SJ, White JK, Steel KP. Mouse screen reveals multiple new genes underlying mouse and human hearing loss. PLoS Biol 2019; 17:e3000194. [PMID: 30973865 PMCID: PMC6459510 DOI: 10.1371/journal.pbio.3000194] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [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: 11/06/2018] [Accepted: 03/07/2019] [Indexed: 11/23/2022] Open
Abstract
Adult-onset hearing loss is very common, but we know little about the underlying molecular pathogenesis impeding the development of therapies. We took a genetic approach to identify new molecules involved in hearing loss by screening a large cohort of newly generated mouse mutants using a sensitive electrophysiological test, the auditory brainstem response (ABR). We review here the findings from this screen. Thirty-eight unexpected genes associated with raised thresholds were detected from our unbiased sample of 1,211 genes tested, suggesting extreme genetic heterogeneity. A wide range of auditory pathophysiologies was found, and some mutant lines showed normal development followed by deterioration of responses, revealing new molecular pathways involved in progressive hearing loss. Several of the genes were associated with the range of hearing thresholds in the human population and one, SPNS2, was involved in childhood deafness. The new pathways required for maintenance of hearing discovered by this screen present new therapeutic opportunities. This study uses an electrophysiological screen of over a thousand new mutant mouse lines to identify 38 new genes underlying deafness, some associated with human hearing function, revealing a wide range of molecular and pathological mechanisms. Progressive hearing loss with age is extremely common in the population, leading to difficulties in understanding speech, increased social isolation, and associated depression. We know it has a significant heritability, but so far we know very little about the molecular pathways leading to hearing loss, hampering the development of treatments. Here, we describe a large-scale screen of 1,211 new targeted mouse mutant lines, resulting in the identification of 38 genes underlying hearing loss that were not previously suspected of involvement in hearing. Some of these genes reveal molecular pathways that may be useful targets for drug development. Our further analysis of the genes identified and the varied pathological mechanisms within the ear resulting from the mutations suggests that hearing loss is an extremely heterogeneous disorder and may have as many as 1,000 genes involved.
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Affiliation(s)
- Neil J. Ingham
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | | | | | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Morag A. Lewis
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Jing Chen
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Annalisa Buniello
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Lorenzo Preite
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Chi Chung Lam
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Felix D. Weiss
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Zӧe Powis
- Department of Emerging Genetics Medicine, Ambry Genetics, Aliso Viejo, California, United States of America
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, United States of America
| | | | - Sally J. Dawson
- UCL Ear Institute, University College London, London, United Kingdom
| | | | - Karen P. Steel
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- * E-mail:
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22
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Geuther BQ, Deats SP, Fox KJ, Murray SA, Braun RE, White JK, Chesler EJ, Lutz CM, Kumar V. Robust mouse tracking in complex environments using neural networks. Commun Biol 2019; 2:124. [PMID: 30937403 PMCID: PMC6440983 DOI: 10.1038/s42003-019-0362-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 06/17/2018] [Accepted: 02/26/2019] [Indexed: 01/21/2023] Open
Abstract
The ability to track animals accurately is critical for behavioral experiments. For video-based assays, this is often accomplished by manipulating environmental conditions to increase contrast between the animal and the background in order to achieve proper foreground/background detection (segmentation). Modifying environmental conditions for experimental scalability opposes ethological relevance. The biobehavioral research community needs methods to monitor behaviors over long periods of time, under dynamic environmental conditions, and in animals that are genetically and behaviorally heterogeneous. To address this need, we applied a state-of-the-art neural network-based tracker for single mice. We compare three different neural network architectures across visually diverse mice and different environmental conditions. We find that an encoder-decoder segmentation neural network achieves high accuracy and speed with minimal training data. Furthermore, we provide a labeling interface, labeled training data, tuned hyperparameters, and a pretrained network for the behavior and neuroscience communities.
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Affiliation(s)
- Brian Q. Geuther
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Sean P. Deats
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Kai J. Fox
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Steve A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | | | | | - Cathleen M. Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Vivek Kumar
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
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23
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Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Kent Lloyd KC, Murphy CJ, Moshiri A. Erratum: Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts. Commun Biol 2019; 2:97. [PMID: 30854487 PMCID: PMC6405960 DOI: 10.1038/s42003-019-0349-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lionel Sebbag
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Sydney G Edwards
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Ann Cooper
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ewan Straiton
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Christopher Reilly
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Stephen M Griffey
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lynette Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - David Clary
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Michel J Roux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Hamid Meziane
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Celeste Owen
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Mohammed Eskandarian
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan J Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vivek Philip
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sharon Clementson-Mobbs
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Russell Joynson
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - 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
| | | | | | - Damian Smedley
- Clinical Pharmacology, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J K 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, 08826, South Korea
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, I-00015, Monterotondo Scalo, Italy
| | - Mark Moore
- International Mouse Phenotyping Consortium, San Anselmo, CA, 94960, USA
| | | | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | | | - Mark P Krebs
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA. .,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
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24
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Goodwin LO, Splinter E, Davis TL, Urban R, He H, Braun RE, Chesler EJ, Kumar V, van Min M, Ndukum J, Philip VM, Reinholdt LG, Svenson K, White JK, Sasner M, Lutz C, Murray SA. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis. Genome Res 2019; 29:494-505. [PMID: 30659012 PMCID: PMC6396414 DOI: 10.1101/gr.233866.117] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/14/2019] [Indexed: 01/05/2023]
Abstract
Transgenesis has been a mainstay of mouse genetics for over 30 yr, providing numerous models of human disease and critical genetic tools in widespread use today. Generated through the random integration of DNA fragments into the host genome, transgenesis can lead to insertional mutagenesis if a coding gene or an essential element is disrupted, and there is evidence that larger scale structural variation can accompany the integration. The insertion sites of only a tiny fraction of the thousands of transgenic lines in existence have been discovered and reported, due in part to limitations in the discovery tools. Targeted locus amplification (TLA) provides a robust and efficient means to identify both the insertion site and content of transgenes through deep sequencing of genomic loci linked to specific known transgene cassettes. Here, we report the first large-scale analysis of transgene insertion sites from 40 highly used transgenic mouse lines. We show that the transgenes disrupt the coding sequence of endogenous genes in half of the lines, frequently involving large deletions and/or structural variations at the insertion site. Furthermore, we identify a number of unexpected sequences in some of the transgenes, including undocumented cassettes and contaminating DNA fragments. We demonstrate that these transgene insertions can have phenotypic consequences, which could confound certain experiments, emphasizing the need for careful attention to control strategies. Together, these data show that transgenic alleles display a high rate of potentially confounding genetic events and highlight the need for careful characterization of each line to assure interpretable and reproducible experiments.
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Affiliation(s)
| | | | | | - Rachel Urban
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Hao He
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA
| | | | | | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Max van Min
- Cergentis B.V., 3584 CM Utrecht, The Netherlands
| | - Juliet Ndukum
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | - Karen Svenson
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | | | - Cathleen Lutz
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
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25
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Moore BA, Leonard BC, Sebbag L, Edwards SG, Cooper A, Imai DM, Straiton E, Santos L, Reilly C, Griffey SM, Bower L, Clary D, Mason J, Roux MJ, Meziane H, Herault Y, McKerlie C, Flenniken AM, Nutter LMJ, Berberovic Z, Owen C, Newbigging S, Adissu H, Eskandarian M, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gallegos JJ, Seavitt JR, Heaney JD, Beaudet AL, Dickinson ME, Justice MJ, Philip V, Kumar V, Svenson KL, Braun RE, Wells S, Cater H, Stewart M, Clementson-Mobbs S, Joynson R, Gao X, Suzuki T, Wakana S, Smedley D, Seong JK, Tocchini-Valentini G, Moore M, Fletcher C, Karp N, Ramirez-Solis R, White JK, de Angelis MH, Wurst W, Thomasy SM, Flicek P, Parkinson H, Brown SDM, Meehan TF, Nishina PM, Murray SA, Krebs MP, Mallon AM, Lloyd KCK, Murphy CJ, Moshiri A. Identification of genes required for eye development by high-throughput screening of mouse knockouts. Commun Biol 2018; 1:236. [PMID: 30588515 PMCID: PMC6303268 DOI: 10.1038/s42003-018-0226-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from the International Mouse Phenotyping Consortium, a large-scale functional genetic screen with the goal of generating and phenotyping a null mutant for every mouse gene. Of 4364 genes evaluated, 347 were identified to influence ocular phenotypes, 75% of which are entirely novel in ocular pathology. This discovery greatly increases the current number of genes known to contribute to ophthalmic disease, and it is likely that many of the genes will subsequently prove to be important in human ocular development and disease. Bret Moore et al. from the International Mouse Phenotyping Consortium report the identification of 347 mouse genes that influence ocular phenotypes when knocked out. 75% of the identified genes have not previously been associated with any ocular pathology.
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Affiliation(s)
- Bret A Moore
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Brian C Leonard
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lionel Sebbag
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Sydney G Edwards
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Ann Cooper
- William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California-Davis, Davis, 95616, CA, USA
| | - Denise M Imai
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Ewan Straiton
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Christopher Reilly
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Stephen M Griffey
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - Lynette Bower
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - David Clary
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Michel J Roux
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Hamid Meziane
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.,CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), CNRS, INSERM, University of Strasbourg, 1 rue Laurent Fries, 67404, Illkirch-Graffenstaden, France
| | | | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Zorana Berberovic
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Celeste Owen
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Susan Newbigging
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Hibret Adissu
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Mohammed Eskandarian
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juan J Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, ON, M5T 3H7, Canada.,The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vivek Philip
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Sharon Clementson-Mobbs
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Russell Joynson
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - 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
| | | | | | - Damian Smedley
- Clinical Pharmacology, Charterhouse Square, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - J K 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, 08826, South Korea
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, Adriano Buzzati-Traverso Campus, Via Ramarini, I-00015, Monterotondo Scalo, Italy
| | - Mark Moore
- International Mouse Phenotyping Consortium, San Anselmo, CA, 94960, USA
| | | | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ramiro Ramirez-Solis
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | | | - Mark P Krebs
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetis Unit and Mary Lyon Center, Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, and Department of Surgery, School of Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA. .,Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, U.C. Davis, Sacramento, CA, 95817, USA.
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26
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Baaten CCFMJ, Meacham S, de Witt SM, Feijge MAH, Adams DJ, Akkerman JWN, Cosemans JMEM, Grassi L, Jupe S, Kostadima M, Mattheij NJA, Prins MH, Ramirez-Solis R, Soehnlein O, Swieringa F, Weber C, White JK, Ouwehand WH, Heemskerk JWM. A synthesis approach of mouse studies to identify genes and proteins in arterial thrombosis and bleeding. Blood 2018; 132:e35-e46. [PMID: 30275110 PMCID: PMC6293874 DOI: 10.1182/blood-2018-02-831982] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/19/2018] [Indexed: 12/25/2022] Open
Abstract
Antithrombotic therapies reduce cardiovascular diseases by preventing arterial thrombosis and thromboembolism, but at expense of increased bleeding risks. Arterial thrombosis studies using genetically modified mice have been invaluable for identification of new molecular targets. Because of low sample sizes and heterogeneity in approaches or methodologies, a formal meta-analysis to compare studies of mice with single-gene defects encountered major limitations. To overcome these, we developed a novel synthesis approach to quantitatively scale 1514 published studies of arterial thrombus formation (in vivo and in vitro), thromboembolism, and tail-bleeding of genetically modified mice. Using a newly defined consistency parameter (CP), indicating the strength of published data, comparisons were made of 431 mouse genes, of which 17 consistently contributed to thrombus formation without affecting hemostasis. Ranking analysis indicated high correlations between collagen-dependent thrombosis models in vivo (FeCl3 injury or ligation/compression) and in vitro. Integration of scores and CP values resulted in a network of protein interactions in thrombosis and hemostasis (PITH), which was combined with databases of genetically linked human bleeding and thrombotic disorders. The network contained 2946 nodes linked to modifying genes of thrombus formation, mostly with expression in megakaryocytes. Reactome pathway analysis and network characteristics revealed multiple novel genes with potential contribution to thrombosis/hemostasis. Studies with additional knockout mice revealed that 4 of 8 (Apoe, Fpr2, Ifnar1, Vps13a) new genes were modifying in thrombus formation. The PITH network further: (i) revealed a high similarity of murine and human hemostatic and thrombotic processes and (ii) identified multiple new candidate proteins regulating these processes.
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Affiliation(s)
- Constance C F M J Baaten
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Institute for Molecular Cardiovascular Research (IMCAR), University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Stuart Meacham
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge, United Kingdom
| | - Susanne M de Witt
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Marion A H Feijge
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Jan-Willem N Akkerman
- Laboratory of Clinical Chemistry and Haematology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Judith M E M Cosemans
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Luigi Grassi
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge, United Kingdom
| | - Steve Jupe
- EMBL-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge, United Kingdom
| | - Nadine J A Mattheij
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Martin H Prins
- Department of Clinical Epidemiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Oliver Soehnlein
- Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University, Munich, Germany
- DZHK, Partner Site Munich Heart Alliance, Munich, Germany; and
- Department of Pathology, AMC, Amsterdam, The Netherlands
| | - Frauke Swieringa
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University, Munich, Germany
- DZHK, Partner Site Munich Heart Alliance, Munich, Germany; and
| | | | - Willem H Ouwehand
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
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27
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Balmus G, Larrieu D, Barros AC, Collins C, Abrudan M, Demir M, Geisler NJ, Lelliott CJ, White JK, Karp NA, Atkinson J, Kirton A, Jacobsen M, Clift D, Rodriguez R, Adams DJ, Jackson SP. Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome. Nat Commun 2018; 9:1700. [PMID: 29703891 PMCID: PMC5923383 DOI: 10.1038/s41467-018-03770-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 09/25/2017] [Accepted: 03/12/2018] [Indexed: 02/02/2023] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, but devastating genetic disease characterized by segmental premature aging, with cardiovascular disease being the main cause of death. Cells from HGPS patients accumulate progerin, a permanently farnesylated, toxic form of Lamin A, disrupting the nuclear shape and chromatin organization, leading to DNA-damage accumulation and senescence. Therapeutic approaches targeting farnesylation or aiming to reduce progerin levels have provided only partial health improvements. Recently, we identified Remodelin, a small-molecule agent that leads to amelioration of HGPS cellular defects through inhibition of the enzyme N-acetyltransferase 10 (NAT10). Here, we show the preclinical data demonstrating that targeting NAT10 in vivo, either via chemical inhibition or genetic depletion, significantly enhances the healthspan in a Lmna G609G HGPS mouse model. Collectively, the data provided here highlights NAT10 as a potential therapeutic target for HGPS.
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Affiliation(s)
- Gabriel Balmus
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Delphine Larrieu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Ana C Barros
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Casey Collins
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Monica Abrudan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nicola J Geisler
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | | | - Natasha A Karp
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - James Atkinson
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 23AT, UK
| | - Andrea Kirton
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Matt Jacobsen
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 23AT, UK
| | - Dean Clift
- Laboratory of Molecular Biology, Cambridge, CB2 OQH, UK
| | - Raphael Rodriguez
- Institut Curie, PSL Research University, Paris Cedex 05, France
- CNRS UMR3666, 75005, Paris, France
- INSERM U1143, 75005, Paris, France
| | - David J Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
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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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Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, Meehan TF, Weninger WJ, Westerberg H, Adissu H, Baker CN, Bower L, Brown JM, Caddle LB, Chiani F, Clary D, Cleak J, Daly MJ, Denegre JM, Doe B, Dolan ME, Edie Helmut Fuchs SM, Gailus-Durner V, Galli A, Gambadoro A, Gallegos J, Guo S, Horner NR, Hsu CW, Johnson SJ, Kalaga S, Keith LC, Lanoue L, Lawson TN, Lek M, Mark M, Marschall S, Mason J, McElwee ML, Nutter SNLMJ, Peterson KA, Ramirez-Solis R, Rowland DJ, Ryder E, Samocha KE, Seavitt JR, Selloum M, Szoke-Kovacs Z, Tamura M, Trainor AG, Tudose I, Wakana S, Warren J, Wendling O, West DB, Wong L, Yoshiki A, Wurst W, MacArthur DG, Tocchini-Valentini GP, Gao X, Flicek P, Bradley A, Skarnes WC, Justice MJ, Parkinson HE, Moore M, Wells S, Braun RE, Svenson KL, de Angelis MH, Herault Y, Mohun T, Mallon AM, Henkelman RM, Brown SDM, Adams DJ, Lloyd KCK, McKerlie C, Beaudet AL, Murray MBSA. Corrigendum: High-throughput discovery of novel developmental phenotypes. Nature 2017; 551:398. [PMID: 29144450 DOI: 10.1038/nature24643] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This corrects the article DOI: 10.1038/nature19356.
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30
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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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31
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Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MHD, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. Prevalence of sexual dimorphism in mammalian phenotypic traits. Nat Commun 2017. [PMID: 28650954 PMCID: PMC5490203 DOI: 10.1038/ncomms15475] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The role of sex in biomedical studies has often been overlooked, despite evidence of sexually dimorphic effects in some biological studies. Here, we used high-throughput phenotype data from 14,250 wildtype and 40,192 mutant mice (representing 2,186 knockout lines), analysed for up to 234 traits, and found a large proportion of mammalian traits both in wildtype and mutants are influenced by sex. This result has implications for interpreting disease phenotypes in animal models and humans. Systemic dissection of sexually dimorphic phenotypes in mice is lacking. Here, Karp and the International Mouse Phenotype Consortium show that approximately 10% of qualitative traits and 56% of quantitative traits in mice as measured in laboratory setting are sexually dimorphic.
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Affiliation(s)
- Natasha A Karp
- Mouse Informatics Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Quantitative Biology, AstraZeneca, Unit 310, Cambridge Science Park, Cambridge CB4 0WG, UK
| | - Jeremy Mason
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Arthur L Beaudet
- Human and Molecular Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Yoav Benjamini
- Department of Statistics and O.R. School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lynette Bower
- Mouse Biology Program, University of California, 2795 Second Street, Suite 400, Davis, California 95618, USA
| | - Robert E Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
| | | | - Elissa J Chesler
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
| | - Mary E Dickinson
- Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Ann M Flenniken
- The Centre for Phenogenomics, 25 Orde Street, Toronto, Ontario, Canada M5T 3H7
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany.,School of Life Science Weihenstephan, Technische Universität München, Alte Akademie 8, Freising 85354, Germany.,German Center for Diabetes Research (DZD), Ingostädter Landstr. 1, Neuherberg 85764, Germany
| | - Xiang Gao
- Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou, Nanjing, Jiangsu 210061, China
| | - Shiying Guo
- Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou, Nanjing, Jiangsu 210061, China
| | | | - Ruth Heller
- Department of Statistics and O.R. School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 Rue Laurent Fries, Illkirch 67404, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch 67404, France.,Centre National de la Recherche Scientifique, UMR7104, 1 rue Laurent Fries, Illkirch 67404, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1 rue Laurent Fries, Illkirch 67404, France.,Université de Strasbourg, 1 rue Laurent Fries, Illkirch 67404, France
| | - Monica J Justice
- The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
| | - Natalja Kurbatova
- Department of Statistics and O.R. School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Christopher J Lelliott
- Mouse Genetics Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, 2795 Second Street, Suite 400, Davis, California 95618, USA
| | | | - Judith E Mank
- Department of Genetics, Evolution &Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Hiroshi Masuya
- BioResource Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Colin McKerlie
- The Centre for Phenogenomics, 25 Orde Street, Toronto, Ontario, Canada M5T 3H7.,The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario, Canada M5G 0A4
| | - Terrence F Meehan
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard F Mott
- Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Stephen A Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
| | - Helen Parkinson
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ramiro Ramirez-Solis
- Mouse Genetics Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Luis Santos
- MRC Harwell Institute, Harwell Campus, Harwell OX11 0RD, UK
| | - John R Seavitt
- Human and Molecular Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Damian Smedley
- Clinical Pharmacology, Queen Mary University of London, Gower Street, London WC1E 6BT, UK
| | - Tania Sorg
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris, 1 Rue Laurent Fries, Illkirch 67404, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 Rue Laurent Fries, Illkirch 67404, France.,Centre National de la Recherche Scientifique, UMR7104, 1 rue Laurent Fries, Illkirch 67404, France.,Institut National de la Santé et de la Recherche Médicale, U964, 1 rue Laurent Fries, Illkirch 67404, France.,Université de Strasbourg, 1 rue Laurent Fries, Illkirch 67404, France
| | - Anneliese O Speak
- Mouse Genetics Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Karen P Steel
- Mouse Genetics Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Wolfson Wing, Hodgkin Building, Guys Campus, London SE1 1UL, UK
| | - Karen L Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
| | | | - Shigeharu Wakana
- BioResource Center, RIKEN, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - David West
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, California 94609, USA
| | - Sara Wells
- MRC Harwell Institute, Harwell Campus, Harwell OX11 0RD, UK
| | | | - Shay Yaacoby
- Department of Statistics and O.R. School of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jacqueline K White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA.,Mouse Genetics Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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32
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Cambridge EL, McIntyre Z, Clare S, Arends MJ, Goulding D, Isherwood C, Caetano SS, Reviriego CB, Swiatkowska A, Kane L, Harcourt K, Adams DJ, White JK, Speak AO. The AMP-activated protein kinase beta 1 subunit modulates erythrocyte integrity. Exp Hematol 2016; 45:64-68.e5. [PMID: 27666489 PMCID: PMC5823972 DOI: 10.1016/j.exphem.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 12/03/2022]
Abstract
Failure to maintain a normal in vivo erythrocyte half-life results in the development of hemolytic anemia. Half-life is affected by numerous factors, including energy balance, electrolyte gradients, reactive oxygen species, and membrane plasticity. The heterotrimeric AMP-activated protein kinase (AMPK) is an evolutionarily conserved serine/threonine kinase that acts as a critical regulator of cellular energy balance. Previous roles for the alpha 1 and gamma 1 subunits in the control of erythrocyte survival have been reported. In the work described here, we studied the role of the beta 1 subunit in erythrocytes and observed microcytic anemia with compensatory extramedullary hematopoiesis together with splenomegaly and increased osmotic resistance. Prkab1tm1b/tm1b mice were generated and phenotyped. Prkab1tm1b/tm1b mice presented with microcytic anemia. Erythrocytes lacking Prkab1 have a variable morphologic appearance. Prkab1-deficient erythrocytes have increased osmotic resistance. The importance of the beta 1 isoform in erythrocyte integrity is discussed.
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Affiliation(s)
- Emma L Cambridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zoe McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Centre for Comparative Pathology, Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Christopher Isherwood
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Susana S Caetano
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Agnieszka Swiatkowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Leanne Kane
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Katherine Harcourt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | -
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
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33
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Ingham NJ, Carlisle F, Pearson S, Lewis MA, Buniello A, Chen J, Isaacson RL, Pass J, White JK, Dawson SJ, Steel KP. S1PR2 variants associated with auditory function in humans and endocochlear potential decline in mouse. Sci Rep 2016; 6:28964. [PMID: 27383011 PMCID: PMC4935955 DOI: 10.1038/srep28964] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/07/2016] [Indexed: 12/29/2022] Open
Abstract
Progressive hearing loss is very common in the population but we still know little about the underlying pathology. A new spontaneous mouse mutation (stonedeaf, stdf ) leading to recessive, early-onset progressive hearing loss was detected and exome sequencing revealed a Thr289Arg substitution in Sphingosine-1-Phosphate Receptor-2 (S1pr2). Mutants aged 2 weeks had normal hearing sensitivity, but at 4 weeks most showed variable degrees of hearing impairment, which became severe or profound in all mutants by 14 weeks. Endocochlear potential (EP) was normal at 2 weeks old but was reduced by 4 and 8 weeks old in mutants, and the stria vascularis, which generates the EP, showed degenerative changes. Three independent mouse knockout alleles of S1pr2 have been described previously, but this is the first time that a reduced EP has been reported. Genomic markers close to the human S1PR2 gene were significantly associated with auditory thresholds in the 1958 British Birth Cohort (n = 6099), suggesting involvement of S1P signalling in human hearing loss. The finding of early onset loss of EP gives new mechanistic insight into the disease process and suggests that therapies for humans with hearing loss due to S1P signalling defects need to target strial function.
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Affiliation(s)
- Neil J Ingham
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Francesca Carlisle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Selina Pearson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Morag A Lewis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Annalisa Buniello
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Jing Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Rivka L Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Johanna Pass
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sally J Dawson
- UCL Ear Institute, University College London, 332 Gray's Inn Road, London WC1X 8EE, UK
| | - Karen P Steel
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Wolfson Centre for Age-Related Diseases, King's College London, Guys Campus, London, SE1 1UL, UK
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34
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Buniello A, Ingham NJ, Lewis MA, Huma AC, Martinez-Vega R, Varela-Nieto I, Vizcay-Barrena G, Fleck RA, Houston O, Bardhan T, Johnson SL, White JK, Yuan H, Marcotti W, Steel KP. Wbp2 is required for normal glutamatergic synapses in the cochlea and is crucial for hearing. EMBO Mol Med 2016; 8:191-207. [PMID: 26881968 PMCID: PMC4772953 DOI: 10.15252/emmm.201505523] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 06/09/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023] Open
Abstract
WBP2 encodes the WW domain-binding protein 2 that acts as a transcriptional coactivator for estrogen receptor α (ESR1) and progesterone receptor (PGR). We reported that the loss of Wbp2 expression leads to progressive high-frequency hearing loss in mouse, as well as in two deaf children, each carrying two different variants in the WBP2 gene. The earliest abnormality we detect in Wbp2-deficient mice is a primary defect at inner hair cell afferent synapses. This study defines a new gene involved in the molecular pathway linking hearing impairment to hormonal signalling and provides new therapeutic targets.
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Affiliation(s)
- Annalisa Buniello
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Neil J Ingham
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Morag A Lewis
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Andreea C Huma
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Raquel Martinez-Vega
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Unit 761, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Varela-Nieto
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, Madrid, Spain Centre for Biomedical Network Research on Rare Diseases (CIBERER), Unit 761, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Roland A Fleck
- Centre for Ultrastructural Imaging, King's College London, London, UK
| | - Oliver Houston
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Tanaya Bardhan
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Stuart L Johnson
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Huijun Yuan
- Medical Genetics Center, Southwest Hospital Third Military Medical University, Chongqing, China
| | - Walter Marcotti
- Department of Biomedical Science, University of Sheffield, Sheffield, UK
| | - Karen P Steel
- Wolfson Centre For Age-Related Diseases, King's College London, London, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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35
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Oellrich A, Meehan TF, Parkinson H, Sarntivijai S, White JK, Karp NA. Reporting phenotypes in mouse models when considering body size as a potential confounder. J Biomed Semantics 2016; 7:2. [PMID: 26865945 PMCID: PMC4748495 DOI: 10.1186/s13326-016-0050-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 10/21/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023] Open
Abstract
Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect phenotype data for a knockout mouse strain of every protein coding gene. The scale of the project requires an automatic analysis pipeline to detect abnormal phenotypes, and disseminate the resulting gene-phenotype annotation data into public resources. A body weight phenotype is a common result of knockout studies. As body weight correlates with many other biological traits, this challenges the interpretation of related gene-phenotype associations. Co-correlation can lead to gene-phenotype associations that are potentially misleading. Here we use statistical modelling to account for body weight as a potential confounder to assess the impact. We find that there is a considerable impact on previously established gene-phenotype associations due to an increase in sensitivity as well as the confounding effect. We investigated the existing ontologies to represent this phenotypic information and we explored ways to ontologically represent the results of the influence of confounders on gene-phenotype associations. With the scale of data being disseminated within the high throughput programs and the range of downstream studies that utilise these data, it is critical to consider how we improve the quality of the disseminated data and provide a robust ontological representation.
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Affiliation(s)
- Anika Oellrich
- />Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire UK
- />Social Genetic & Developmental Psychiatry, King’s College London, London, UK
| | - Terrence F. Meehan
- />Samples, Phenotypes and Ontologies, European Molecular Biology Laboratory—European Bioinformatics Institute, Hinxton, Cambridge UK
| | - Helen Parkinson
- />Samples, Phenotypes and Ontologies, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Sirarat Sarntivijai
- />Samples, Phenotypes and Ontologies, European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
- />The Centre for Therapeutic Target Validation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Jacqueline K. White
- />Mouse Genetics Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire UK
| | - Natasha A. Karp
- />Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire UK
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Joyce PI, Fratta P, Landman AS, Mcgoldrick P, Wackerhage H, Groves M, Busam BS, Galino J, Corrochano S, Beskina OA, Esapa C, Ryder E, Carter S, Stewart M, Codner G, Hilton H, Teboul L, Tucker J, Lionikas A, Estabel J, Ramirez-Solis R, White JK, Brandner S, Plagnol V, Bennet DLH, Abramov AY, Greensmith L, Fisher EMC, Acevedo-Arozena A. Deficiency of the zinc finger protein ZFP106 causes motor and sensory neurodegeneration. Hum Mol Genet 2015; 25:291-307. [PMID: 26604141 PMCID: PMC4706115 DOI: 10.1093/hmg/ddv471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/11/2015] [Indexed: 12/12/2022] Open
Abstract
Zinc finger motifs are distributed amongst many eukaryotic protein families, directing nucleic acid–protein and protein–protein interactions. Zinc finger protein 106 (ZFP106) has previously been associated with roles in immune response, muscle differentiation, testes development and DNA damage, although little is known about its specific function. To further investigate the function of ZFP106, we performed an in-depth characterization of Zfp106 deficient mice (Zfp106−/−), and we report a novel role for ZFP106 in motor and sensory neuronal maintenance and survival. Zfp106−/− mice develop severe motor abnormalities, major deficits in muscle strength and histopathological changes in muscle. Intriguingly, despite being highly expressed throughout the central nervous system, Zfp106−/− mice undergo selective motor and sensory neuronal and axonal degeneration specific to the spinal cord and peripheral nervous system. Neurodegeneration does not occur during development of Zfp106−/− mice, suggesting that ZFP106 is likely required for the maintenance of mature peripheral motor and sensory neurons. Analysis of embryonic Zfp106−/− motor neurons revealed deficits in mitochondrial function, with an inhibition of Complex I within the mitochondrial electron transport chain. Our results highlight a vital role for ZFP106 in sensory and motor neuron maintenance and reveal a novel player in mitochondrial dysfunction and neurodegeneration.
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Affiliation(s)
- Peter I Joyce
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Pietro Fratta
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Philip Mcgoldrick
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Michael Groves
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Jorge Galino
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | | | - Olga A Beskina
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - Edward Ryder
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Sarah Carter
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Gemma Codner
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Helen Hilton
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Lydia Teboul
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | - Jennifer Tucker
- MRC Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK
| | | | - Jeanne Estabel
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Ramiro Ramirez-Solis
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Jacqueline K White
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and
| | - Sebastian Brandner
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | | | - David L H Bennet
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Andrey Y Abramov
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
| | - Linda Greensmith
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
| | - Elizabeth M C Fisher
- UCL Institute of Neurology and MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK,
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Jadeja S, Barnard AR, McKie L, Cross SH, White JK, Robertson M, Budd PS, MacLaren RE, Jackson IJ. Mouse slc9a8 mutants exhibit retinal defects due to retinal pigmented epithelium dysfunction. Invest Ophthalmol Vis Sci 2015; 56:3015-26. [PMID: 25736793 DOI: 10.1167/iovs.14-15735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
PURPOSE As part of a large scale systematic screen to determine the effects of gene knockout mutations in mice, a retinal phenotype was found in mice lacking the Slc9a8 gene, encoding the sodium/hydrogen ion exchange protein NHE8. We aimed to characterize the mutant phenotype and the role of sodium/hydrogen ion exchange in retinal function. METHODS Detailed histology characterized the pathological consequences of Slc9a8 mutation, and retinal function was assessed by electroretinography (ERG). A conditional allele was used to identify the cells in which NHE8 function is critical for retinal function, and mutant cells analyzed for the effect of the mutation on endosomes. RESULTS Histology of mutant retinas reveals a separation of photoreceptors from the RPE and infiltration by macrophages. There is a small reduction in photoreceptor length and a mislocalization of visual pigments. The ERG testing reveals a deficit in rod and cone pathway function. The RPE shows abnormal morphology, and mutation of Slc9a8 in only RPE cells recapitulates the mutant phenotype. The NHE8 protein localizes to endosomes, and mutant cells have much smaller recycling endosomes. CONCLUSIONS The NHE8 protein is required in the RPE to maintain correct regulation of endosomal volume and/or pH which is essential for the cellular integrity and subsequent function of RPE.
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Affiliation(s)
- Shalini Jadeja
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alun R Barnard
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sally H Cross
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Morag Robertson
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter S Budd
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Ian J Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom 4Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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Tuck E, Estabel J, Oellrich A, Maguire AK, Adissu HA, Souter L, Siragher E, Lillistone C, Green AL, Wardle-Jones H, Carragher DM, Karp NA, Smedley D, Adams NC, Bussell JN, Adams DJ, Ramírez-Solis R, Steel KP, Galli A, White JK. A gene expression resource generated by genome-wide lacZ profiling in the mouse. Dis Model Mech 2015; 8:1467-78. [PMID: 26398943 PMCID: PMC4631787 DOI: 10.1242/dmm.021238] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/10/2015] [Indexed: 01/26/2023] Open
Abstract
Knowledge of the expression profile of a gene is a critical piece of information required to build an understanding of the normal and essential functions of that gene and any role it may play in the development or progression of disease. High-throughput, large-scale efforts are on-going internationally to characterise reporter-tagged knockout mouse lines. As part of that effort, we report an open access adult mouse expression resource, in which the expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter gene. Many specific and informative expression patterns were noted. Expression was most commonly observed in the testis and brain and was most restricted in white adipose tissue and mammary gland. Over half of the assessed genes presented with an absent or localised expression pattern (categorised as 0-10 positive structures). A link between complexity of expression profile and viability of homozygous null animals was observed; inactivation of genes expressed in ≥ 21 structures was more likely to result in reduced viability by postnatal day 14 compared with more restricted expression profiles. For validation purposes, this mouse expression resource was compared with Bgee, a federated composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set. Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource.
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Affiliation(s)
- Elizabeth Tuck
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jeanne Estabel
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Anika Oellrich
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Hibret A Adissu
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, 25 Orde Street, Toronto, Canada M5T 3H7
| | - Luke Souter
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Angela L Green
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | | | - Natasha A Karp
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Damian Smedley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Niels C Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - James N Bussell
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Karen P Steel
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Antonella Galli
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
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Salsbury G, Cambridge EL, McIntyre Z, Arends MJ, Karp NA, Isherwood C, Shannon C, Hooks Y, Ramirez-Solis R, Adams DJ, White JK, Speak AO. Corrigendum to "Disruption of the potassium channel regulatory subunit KCNE2 causes iron-deficient anemia" [Experimental Hematology, Vol. 42, Issue 12, p1053-1058.e1]. Exp Hematol 2015; 43:424. [PMID: 28843321 PMCID: PMC5597554 DOI: 10.1016/j.exphem.2015.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Grace Salsbury
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Emma L Cambridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Zoe McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Natasha A Karp
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Christopher Isherwood
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Carl Shannon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yvette Hooks
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | -
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ramiro Ramirez-Solis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
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Podrini C, Koffas A, Chokshi S, Vinciguerra M, Lelliott CJ, White JK, Adissu HA, Williams R, Greco A. MacroH2A1 isoforms are associated with epigenetic markers for activation of lipogenic genes in fat-induced steatosis. FASEB J 2014; 29:1676-87. [PMID: 25526730 DOI: 10.1096/fj.14-262717] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/24/2014] [Indexed: 01/14/2023]
Abstract
The importance of epigenetic changes in the development of hepatic steatosis is largely unknown. The histone variant macroH2A1 under alternative splicing gives rise to macroH2A1.1 and macroH2A1.2. In this study, we show that the macroH2A1 isoforms play an important role in the regulation of lipid accumulation in hepatocytes. Hepatoma cell line and immortalized human hepatocytes transiently transfected or knocked down with macroH2A1 isoforms were used as in vitro model of fat-induced steatosis. Gene expressions were analyzed by quantitative PCR array and Western blot. Chromatin immunoprecipitation analysis was performed to check the association of histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) with the promoter of lipogenic genes. Livers from knockout mice that are resistant to lipid deposition despite a high-fat diet were used for histopathology. We found that macroH2A1.2 is regulated by fat uptake and that its overexpression caused an increase in lipid uptake, triglycerides, and lipogenic genes compared with macroH2A1.1. This suggests that macroH2A1.2 is important for lipid uptake, whereas macroH2A1.1 was found to be protective. The result was supported by a high positivity for macroH2A1.1 in knockout mice for genes targeted by macroH2A1 (Atp5a1 and Fam73b), that under a high-fat diet presented minimal lipidosis. Moreover, macroH2A1 isoforms differentially regulate the expression of lipogenic genes by modulating the association of the active (H3K4me3) and repressive (H3K27me3) histone marks on their promoters. This study underlines the importance of the replacement of noncanonical histones in the regulation of genes involved in lipid metabolism in the progression of steatosis.
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Affiliation(s)
- Christine Podrini
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Apostolos Koffas
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Shilpa Chokshi
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Manlio Vinciguerra
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Christopher J Lelliott
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Jacqueline K White
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hibret A Adissu
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Roger Williams
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Azzura Greco
- *Foundation for Liver Research, Institute of Hepatology, London, United Kingdom; University College London (UCL)--Institute for Liver & Digestive Health, UCL Medical School, London, United Kingdom, Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; and Physiology and Experimental Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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Chen J, Ingham N, Kelly J, Jadeja S, Goulding D, Pass J, Mahajan VB, Tsang SH, Nijnik A, Jackson IJ, White JK, Forge A, Jagger D, Steel KP. Spinster homolog 2 (spns2) deficiency causes early onset progressive hearing loss. PLoS Genet 2014; 10:e1004688. [PMID: 25356849 PMCID: PMC4214598 DOI: 10.1371/journal.pgen.1004688] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [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: 04/09/2014] [Accepted: 08/19/2014] [Indexed: 12/13/2022] Open
Abstract
Spinster homolog 2 (Spns2) acts as a Sphingosine-1-phosphate (S1P) transporter in zebrafish and mice, regulating heart development and lymphocyte trafficking respectively. S1P is a biologically active lysophospholipid with multiple roles in signalling. The mechanism of action of Spns2 is still elusive in mammals. Here, we report that Spns2-deficient mice rapidly lost auditory sensitivity and endocochlear potential (EP) from 2 to 3 weeks old. We found progressive degeneration of sensory hair cells in the organ of Corti, but the earliest defect was a decline in the EP, suggesting that dysfunction of the lateral wall was the primary lesion. In the lateral wall of adult mutants, we observed structural changes of marginal cell boundaries and of strial capillaries, and reduced expression of several key proteins involved in the generation of the EP (Kcnj10, Kcnq1, Gjb2 and Gjb6), but these changes were likely to be secondary. Permeability of the boundaries of the stria vascularis and of the strial capillaries appeared normal. We also found focal retinal degeneration and anomalies of retinal capillaries together with anterior eye defects in Spns2 mutant mice. Targeted inactivation of Spns2 in red blood cells, platelets, or lymphatic or vascular endothelial cells did not affect hearing, but targeted ablation of Spns2 in the cochlea using a Sox10-Cre allele produced a similar auditory phenotype to the original mutation, suggesting that local Spns2 expression is critical for hearing in mammals. These findings indicate that Spns2 is required for normal maintenance of the EP and hence for normal auditory function, and support a role for S1P signalling in hearing. Progressive hearing loss is common in the human population but we know very little about the molecular mechanisms involved. Mutant mice are useful for investigating these mechanisms and have revealed a wide range of different abnormalities that can all lead to the same outcome: deafness. We report here our findings of a new mouse line with a mutation in the Spns2 gene, affecting the release of a lipid called sphingosine-1-phosphate, which has an important role in several processes in the body. For the first time, we report that this molecular pathway is required for normal hearing through a role in generating a voltage difference that acts like a battery, allowing the sensory hair cells of the cochlea to detect sounds at extremely low levels. Without the normal function of the Spns2 gene and release of sphingosine-1-phosphate locally in the inner ear, the voltage in the cochlea declines, leading to rapid loss of sensitivity to sound and ultimately to complete deafness. The human version of this gene, SPNS2, may be involved in human deafness, and understanding the underlying mechanism presents an opportunity to develop potential treatments for this form of hearing loss.
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Affiliation(s)
- Jing Chen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Neil Ingham
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - John Kelly
- Centre for Auditory Research, UCL Ear Institute, London, United Kingdom
| | - Shalini Jadeja
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom, and Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | - David Goulding
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Johanna Pass
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Vinit B. Mahajan
- Omics Laboratory, University of Iowa, Iowa City, Iowa, United States of America
| | - Stephen H. Tsang
- Edward S. Harkness Eye Institute, Columbia University, New York, New York, United States of America
| | - Anastasia Nijnik
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Department of Physiology, Complex Traits Group, McGill University, Montreal, Quebec, Canada
| | - Ian J. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom, and Roslin Institute, University of Edinburgh, Easter Bush, United Kingdom
| | | | - Andrew Forge
- Centre for Auditory Research, UCL Ear Institute, London, United Kingdom
| | - Daniel Jagger
- Centre for Auditory Research, UCL Ear Institute, London, United Kingdom
| | - Karen P. Steel
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
- * E-mail:
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42
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Karp NA, Speak AO, White JK, Adams DJ, Hrabé de Angelis M, Hérault Y, Mott RF. Impact of temporal variation on design and analysis of mouse knockout phenotyping studies. PLoS One 2014; 9:e111239. [PMID: 25343444 PMCID: PMC4208881 DOI: 10.1371/journal.pone.0111239] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 06/29/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
A significant challenge facing high-throughput phenotyping of in-vivo knockout mice is ensuring phenotype calls are robust and reliable. Central to this problem is selecting an appropriate statistical analysis that models both the experimental design (the workflow and the way control mice are selected for comparison with knockout animals) and the sources of variation. Recently we proposed a mixed model suitable for small batch-oriented studies, where controls are not phenotyped concurrently with mutants. Here we evaluate this method both for its sensitivity to detect phenotypic effects and to control false positives, across a range of workflows used at mouse phenotyping centers. We found the sensitivity and control of false positives depend on the workflow. We show that the phenotypes in control mice fluctuate unexpectedly between batches and this can cause the false positive rate of phenotype calls to be inflated when only a small number of batches are tested, when the effect of knockout becomes confounded with temporal fluctuations in control mice. This effect was observed in both behavioural and physiological assays. Based on this analysis, we recommend two approaches (workflow and accompanying control strategy) and associated analyses, which would be robust, for use in high-throughput phenotyping pipelines. Our results show the importance in modelling all sources of variability in high-throughput phenotyping studies.
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Affiliation(s)
- Natasha A. Karp
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- * E-mail:
| | - Anneliese O. Speak
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | | | - David J. Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Martin Hrabé de Angelis
- German Mouse Clinic - Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Yann Hérault
- Institut Clinique de la Souris, Université de Strasbourg, Illkirch, France
| | - Richard F. Mott
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
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DiTommaso T, Jones LK, Cottle DL, Gerdin AK, Vancollie VE, Watt FM, Ramirez-Solis R, Bradley A, Steel KP, Sundberg JP, White JK, Smyth IM. Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse. PLoS Genet 2014; 10:e1004705. [PMID: 25340873 PMCID: PMC4207618 DOI: 10.1371/journal.pgen.1004705] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 02/14/2014] [Accepted: 08/26/2014] [Indexed: 12/15/2022] Open
Abstract
The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation.
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Affiliation(s)
- Tia DiTommaso
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Australia
| | - Lynelle K. Jones
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Australia
| | - Denny L. Cottle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Australia
| | | | - Anna-Karin Gerdin
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valerie E. Vancollie
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Fiona M. Watt
- Centre for Stem Cells and Regenerative Medicine King's College London, Guy's Hospital, London, United Kingdom
| | - Ramiro Ramirez-Solis
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Karen P. Steel
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London, United Kingdom
| | - John P. Sundberg
- The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Jacqueline K. White
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ian M. Smyth
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, Australia
- * E-mail:
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Adissu HA, Medhanie GA, Morikawa L, White JK, Newbigging S, McKerlie C. Right Ventricular Epicardial Fibrosis in Mice With Sternal Segment Dislocation. Vet Pathol 2014; 52:967-76. [PMID: 25281652 DOI: 10.1177/0300985814552108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report coincident sternal segment dislocation and focally extensive right ventricular epicardial fibrosis observed during routine histopathology evaluation of C57BL/6N mice as part of a high throughput phenotyping screen conducted between 4 and 16 weeks of age. This retrospective case series study was conducted to determine whether cardiac fibrosis was a pathological consequence of sternal segment dislocation. We identified sternal segment dislocation in 51 of the total 1103 mice (4.6%) analyzed at 16 weeks of age. Males were more frequently affected. In all cases but 2, the dislocation occurred at the fourth intersternebral joint. In 42 of the 51 cases (82.4%), the dislocation was encased by regenerative cartilaginous callus that protruded internally into the thoracic cavity (intrathoracic callus) and/or externally to the outer aspect of the sternum (extrathoracic callus). Displacement of dislocated ends of the sternum into the thoracic cavity was present in 19 of 51 cases (36.5%). Coincident minimal or mild right ventricular epicardial and subepicardial fibrosis was observed in 22 of the 51 cases (43%) but was not observed in any of the mice in the absence of sternal segment dislocation. Our data suggest that right ventricular fibrosis was likely caused by direct injury of the right ventricle by the dislocated ends of the sternum and/or by intrathoracic callus that develops post dislocation. Potential pathogenesis for the sternal and cardiac lesions and their implication for the interpretation of phenotypes in mouse models of cardiopulmonary and skeletal disease are discussed.
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Affiliation(s)
- H A Adissu
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, ON, Canada Physiology & Experimental Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - G A Medhanie
- Population Medicine, University of Guelph, Ontario Veterinary College, Guelph, ON, Canada
| | - L Morikawa
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, ON, Canada Physiology & Experimental Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - J K White
- Mouse Genetics Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - S Newbigging
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, ON, Canada Physiology & Experimental Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - C McKerlie
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, Toronto, ON, Canada Physiology & Experimental Medicine Research Program, The Hospital for Sick Children, Toronto, ON, Canada Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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White JK, Nayagum D, Beaven RP. A multi-component two-phase flow algorithm for use in landfill processes modelling. Waste Manag 2014; 34:1644-1656. [PMID: 24925875 DOI: 10.1016/j.wasman.2014.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 03/31/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
This paper describes the finite difference algorithm that has been developed for the flow sub-model of the University of Southampton landfill degradation and transport model LDAT. The liquid and gas phase flow components are first decoupled from the solid phase of the full multi-phase, multi-component landfill process constitutive equations and are then rearranged into a format that can be applied as a calculation procedure within the framework of a three dimensional array of finite difference rectangular elements. The algorithm contains a source term which accommodates the non-flow landfill processes of degradation, gas solubility, and leachate chemical equilibrium, sub-models that have been described in White and Beaven (2013). The paper includes an illustration of the application of the flow sub-model in the context of the leachate recirculation tests carried out at the Beddington landfill project. This illustration demonstrates the ability of the sub-model to track movement in the gas phase as well as the liquid phase, and to simulate multi-directional flow patterns that are different in each of the phases.
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Affiliation(s)
- J K White
- Faculty of Engineering and the Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - D Nayagum
- FEESA Ltd, Westmead House, Westmead, Farnborough, Hants GU14 7LP, UK
| | - R P Beaven
- Faculty of Engineering and the Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
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Salsbury G, Cambridge EL, McIntyre Z, Arends MJ, Karp NA, Isherwood C, Shannon C, Hooks Y, Ramirez-Solis R, Adams DJ, White JK, Speak AO. Disruption of the potassium channel regulatory subunit KCNE2 causes iron-deficient anemia. Exp Hematol 2014; 42:1053-8.e1. [PMID: 25127743 PMCID: PMC4271779 DOI: 10.1016/j.exphem.2014.07.269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/04/2014] [Accepted: 07/08/2014] [Indexed: 12/21/2022]
Abstract
Iron homeostasis is a dynamic process that is tightly controlled to balance iron uptake, storage, and export. Reduction of dietary iron from the ferric to the ferrous form is required for uptake by solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 (Slc11a2) into the enterocytes. Both processes are proton dependent and have led to the suggestion of the importance of acidic gastric pH for the absorption of dietary iron. Potassium voltage-gated channel subfamily E, member 2 (KCNE2), in combination with potassium voltage-gated channel, KQT-like subfamily, member 1 (KCNQ1), form a gastric potassium channel essential for gastric acidification. Deficiency of either Kcne2 or Kcnq1 results in achlorhydia, gastric hyperplasia, and neoplasia, but the impact on iron absorption has not, to our knowledge, been investigated. Here we report that Kcne2-deficient mice, in addition to the previously reported phenotypes, also present with iron-deficient anemia. Interestingly, impaired function of KCNQ1 results in iron-deficient anemia in Jervell and Lange-Nielsen syndrome patients. We speculate that impaired function of KCNE2 could result in the same clinical phenotype.
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Affiliation(s)
- Grace Salsbury
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Emma L Cambridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Zoe McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Natasha A Karp
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Christopher Isherwood
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Carl Shannon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yvette Hooks
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Ramiro Ramirez-Solis
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.
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Liakath-Ali K, Vancollie VE, Heath E, Smedley DP, Estabel J, Sunter D, Ditommaso T, White JK, Ramirez-Solis R, Smyth I, Steel KP, Watt FM. Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen. Nat Commun 2014; 5:3540. [PMID: 24721909 PMCID: PMC3996542 DOI: 10.1038/ncomms4540] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/04/2014] [Indexed: 12/19/2022] Open
Abstract
Permanent stop-and-shop large-scale mouse mutant resources provide an excellent platform to decipher tissue phenogenomics. Here we analyse skin from 538 knockout mouse mutants generated by the Sanger Institute Mouse Genetics Project. We optimize immunolabelling of tail epidermal wholemounts to allow systematic annotation of hair follicle, sebaceous gland and interfollicular epidermal abnormalities using ontology terms from the Mammalian Phenotype Ontology. Of the 50 mutants with an epidermal phenotype, 9 map to human genetic conditions with skin abnormalities. Some mutant genes are expressed in the skin, whereas others are not, indicating systemic effects. One phenotype is affected by diet and several are incompletely penetrant. In-depth analysis of three mutants, Krt76, Myo5a (a model of human Griscelli syndrome) and Mysm1, provides validation of the screen. Our study is the first large-scale genome-wide tissue phenotype screen from the International Knockout Mouse Consortium and provides an open access resource for the scientific community. Large-scale efforts are put into the generation of knockout mutant mice for many individual genes. Here, the authors systematically screen skin from 538 mutant mice and identify 50 mutants with epidermal phenotypes, of which 9 are also associated with human skin defects.
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Affiliation(s)
- Kifayathullah Liakath-Ali
- 1] Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK [2] Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK [3] Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Valerie E Vancollie
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Emma Heath
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Damian P Smedley
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jeanne Estabel
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David Sunter
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Tia Ditommaso
- 1] Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria 3800, Australia [2] Present address: Brigham Regenerative Medicine Center, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Ian Smyth
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Karen P Steel
- 1] Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] Wolfson Centre for Age-Related Diseases, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital, London SE1 9RT, UK
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Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y, Carragher DM, Clarke K, Karp NA, Newbigging S, Jones N, Morikawa L, White JK, McKerlie C. Histopathology reveals correlative and unique phenotypes in a high-throughput mouse phenotyping screen. Dis Model Mech 2014; 7:515-24. [PMID: 24652767 PMCID: PMC4007403 DOI: 10.1242/dmm.015263] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Mouse Genetics Project (MGP) at the Wellcome Trust Sanger Institute aims to generate and phenotype over 800 genetically modified mouse lines over the next 5 years to gain a better understanding of mammalian gene function and provide an invaluable resource to the scientific community for follow-up studies. Phenotyping includes the generation of a standardized biobank of paraffin-embedded tissues for each mouse line, but histopathology is not routinely performed. In collaboration with the Pathology Core of the Centre for Modeling Human Disease (CMHD) we report the utility of histopathology in a high-throughput primary phenotyping screen. Histopathology was assessed in an unbiased selection of 50 mouse lines with (n=30) or without (n=20) clinical phenotypes detected by the standard MGP primary phenotyping screen. Our findings revealed that histopathology added correlating morphological data in 19 of 30 lines (63.3%) in which the primary screen detected a phenotype. In addition, seven of the 50 lines (14%) presented significant histopathology findings that were not associated with or predicted by the standard primary screen. Three of these seven lines had no clinical phenotype detected by the standard primary screen. Incidental and strain-associated background lesions were present in all mutant lines with good concordance to wild-type controls. These findings demonstrate the complementary and unique contribution of histopathology to high-throughput primary phenotyping of mutant mice.
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Affiliation(s)
- Hibret A Adissu
- Centre for Modeling Human Disease, Toronto Centre for Phenogenomics, 25 Orde Street, Toronto, ON M5T 3H7, Canada
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White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP. Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes. Cell 2013; 154:452-64. [PMID: 23870131 PMCID: PMC3717207 DOI: 10.1016/j.cell.2013.06.022] [Citation(s) in RCA: 371] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/10/2013] [Accepted: 06/17/2013] [Indexed: 02/06/2023]
Abstract
Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis. PaperClip
Large openly available resource of targeted mouse mutants and phenotypic data Screen for broad range of disease features and traits Many novel phenotypes suggest functions for both studied and unstudied genes Haploinsufficiency and pleiotropy are common
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White JK, Beaven RP. Developments to a landfill processes model following its application to two landfill modelling challenges. Waste Manag 2013; 33:1969-1981. [PMID: 23318154 DOI: 10.1016/j.wasman.2012.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 11/23/2012] [Accepted: 12/07/2012] [Indexed: 06/01/2023]
Abstract
The landfill model LDAT simulates the transport and bio-chemical behaviour of the solid, liquid and gas phases of waste contained in a landfill. LDAT was applied to the LMC1 and LMC2 landfill modelling challenges held in 2009 and 2011. These were blind modelling challenges with the model acting in a predictive mode based on limited early time sections of full datasets. The LMC1 challenge dataset was from a 0.34m deep 0.48m diameter laboratory test cell, and the LMC2 dataset was from a 55m×80m 8m deep landfill test cell which formed part of the Dutch sustainable landfill research programme at Landgraaf in the Netherlands. The paper describes developments in LDAT arising directly from the experience of responding to the two challenges, and discusses the model input and output data obtained from a calibration using the full datasets. The developments include the modularisation of the model into a set of linked sub-models, the strategy for converting conventional waste characteristics into model input parameters, the identification of flexible degradation pathways to control the CO2:CH4 ratio, and the application of a chemical equilibrium model that includes a stage in which the solid waste components dissolve into the leachate.
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Affiliation(s)
- J K White
- Faculty of Engineering and the Environment, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
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