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Abstract
Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.
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Affiliation(s)
- Philippe Gros
- McGill University Research Center on Complex Traits, Department of Biochemistry, and Department of Human Genetics, McGill University, Montréal, Québec, Canada;
| | - Jean-Laurent Casanova
- Howard Hughes Medical Institute and St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA;
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, and University of Paris Cité, Imagine Institute and Necker Hospital for Sick Children, Paris, France
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2
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Hashimoto D, Fujimoto K, Morioka S, Ayabe S, Kataoka T, Fukumura R, Ueda Y, Kajimoto M, Hyuga T, Suzuki K, Hara I, Asamura S, Wakana S, Yoshiki A, Gondo Y, Tamura M, Sasaki T, Yamada G. Establishment of mouse line showing inducible priapism-like phenotypes. Reprod Med Biol 2022; 21:e12472. [PMID: 35765371 PMCID: PMC9207557 DOI: 10.1002/rmb2.12472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
Purpose Penile research is expected to reveal new targets for treatment and prevention of the complex mechanisms of its disorder including erectile dysfunction (ED). Thus, analyses of the molecular processes of penile ED and continuous erection as priapism are essential issues of reproductive medicine. Methods By performing mouse N‐ethyl‐N‐nitrosourea mutagenesis and exome sequencing, we established a novel mouse line displaying protruded genitalia phenotype (PGP; priapism‐like phenotype) and identified a novel Pitpna gene mutation for PGP. Extensive histological analyses on the Pitpna mutant and intracavernous pressure measurement (ICP) and liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI/MS)/MS analyses were performed. Results We evaluated the role of phospholipids during erection for the first time and showed the mutants of inducible phenotypes of priapism. Moreover, quantitative analysis using LC–ESI/MS/MS revealed that the level of phosphatidylinositol (PI) was significantly lower in the mutant penile samples. These results imply that PI may contribute to penile erection by PITPα. Conclusions Our findings suggest that the current mutant is a mouse model for priapism and abnormalities in PI signaling pathways through PITPα may lead to priapism providing an attractive novel therapeutic target in its treatment.
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Affiliation(s)
- Daiki Hashimoto
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
| | - Kota Fujimoto
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
| | - Shin Morioka
- Department of Biochemical Pathophysiology/Lipid Biology Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan
| | - Shinya Ayabe
- Experimental Animal Division RIKEN BioResource Research Center Ibaraki Japan
| | - Tomoya Kataoka
- Department of Clinical Pharmaceutics Graduate School of Medical Sciences Nagoya City University Nagoya Japan
| | - Ryutaro Fukumura
- Clinical Laboratories Department sSRL & Shizuoka Cancer Center Collaborative Laboratories, Inc Shizuoka Pref Japan
| | - Yuko Ueda
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Urology Wakayama Medical University Wakayama Japan
| | - Mizuki Kajimoto
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
| | - Taiju Hyuga
- Department of Pediatric Urology Children's Medical Center Tochigi Jichi Medical University Tochigi Japan
| | - Kentaro Suzuki
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
| | - Isao Hara
- Department of Urology Wakayama Medical University Wakayama Japan
| | - Shinichi Asamura
- Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
| | - Shigeharu Wakana
- Department of Animal Experimentation Foundation for Biomedical Research and Innovation at Kobe Creative Lab for Innovation in Kobe 5F 6-3-7 Kobe Hyogo Japan
| | - Atsushi Yoshiki
- Experimental Animal Division RIKEN BioResource Research Center Ibaraki Japan
| | - Yoichi Gondo
- Department of Molecular Life Sciences Division of Basic Medical Science and Molecular Medicine Tokai University School of Medicine Isehara-shi Kanagawa Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis RIKEN BioResource Research Center Tsukuba Ibaraki Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology/Lipid Biology Medical Research Institute Tokyo Medical and Dental University (TMDU) Tokyo Japan
| | - Gen Yamada
- Department of Developmental Genetics Institute of Advanced Medicine, Wakayama Medical University Wakayama Japan.,Department of Plastic and Reconstructive Surgery Wakayama Medical University Wakayama Japan
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3
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Rios JJ, Denton K, Yu H, Manickam K, Garner S, Russell J, Ludwig S, Rosenfeld JA, Liu P, Munch J, Sucato DJ, Beutler B, Wise CA. Saturation mutagenesis defines novel mouse models of severe spine deformity. Dis Model Mech 2021; 14:269194. [PMID: 34142127 PMCID: PMC8246263 DOI: 10.1242/dmm.048901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Embryonic formation and patterning of the vertebrate spinal column requires coordination of many molecular cues. After birth, the integrity of the spine is impacted by developmental abnormalities of the skeletal, muscular and nervous systems, which may result in deformities, such as kyphosis and scoliosis. We sought to identify novel genetic mouse models of severe spine deformity by implementing in vivo skeletal radiography as part of a high-throughput saturation mutagenesis screen. We report selected examples of genetic mouse models following radiographic screening of 54,497 mice from 1275 pedigrees. An estimated 30.44% of autosomal genes harbored predicted damaging alleles examined twice or more in the homozygous state. Of the 1275 pedigrees screened, 7.4% presented with severe spine deformity developing in multiple mice, and of these, meiotic mapping implicated N-ethyl-N-nitrosourea alleles in 21% of pedigrees. Our study provides proof of concept that saturation mutagenesis is capable of discovering novel mouse models of human disease, including conditions with skeletal, neural and neuromuscular pathologies. Furthermore, we report a mouse model of skeletal disease, including severe spine deformity, caused by recessive mutation in Scube3. By integrating results with a human clinical exome database, we identified a patient with undiagnosed skeletal disease who harbored recessive mutations in SCUBE3, and we demonstrated that disease-associated mutations are associated with reduced transactivation of Smad signaling in vitro. All radiographic results and mouse models are made publicly available through the Mutagenetix online database with the goal of advancing understanding of spine development and discovering novel mouse models of human disease. Summary: We report selected mouse models of spine deformity following mutagenesis across 30% of autosomal genes, results of which are made publicly available to advance understanding of spine development and disease.
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Affiliation(s)
- Jonathan J Rios
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kristin Denton
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Hao Yu
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Shannon Garner
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Ludwig
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Pengfei Liu
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Baylor Genetics, Houston, TX 77021, USA
| | - Jake Munch
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Daniel J Sucato
- Department of Orthopaedics, Scottish Rite for Children, Dallas, TX 75219, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carol A Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, Dallas, TX 75219, USA.,Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Orthopaedic Surgery, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Portero V, Nicol T, Podliesna S, Marchal GA, Baartscheer A, Casini S, Tadros R, Treur JL, Tanck MWT, Cox IJ, Probert F, Hough TA, Falcone S, Beekman L, Müller-Nurasyid M, Kastenmüller G, Gieger C, Peters A, Kääb S, Sinner MF, Blease A, Verkerk AO, Bezzina CR, Potter PK, Remme CA. Chronically elevated branched chain amino acid levels are pro-arrhythmic. Cardiovasc Res 2021; 118:1742-1757. [PMID: 34142125 PMCID: PMC9215196 DOI: 10.1093/cvr/cvab207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/16/2021] [Indexed: 01/03/2023] Open
Abstract
Aims Cardiac arrhythmias comprise a major health and economic burden and are associated with significant morbidity and mortality, including cardiac failure, stroke, and sudden cardiac death (SCD). Development of efficient preventive and therapeutic strategies is hampered by incomplete knowledge of disease mechanisms and pathways. Our aim is to identify novel mechanisms underlying cardiac arrhythmia and SCD using an unbiased approach. Methods and results We employed a phenotype-driven N-ethyl-N-nitrosourea mutagenesis screen and identified a mouse line with a high incidence of sudden death at young age (6–9 weeks) in the absence of prior symptoms. Affected mice were found to be homozygous for the nonsense mutation Bcat2p.Q300*/p.Q300* in the Bcat2 gene encoding branched chain amino acid transaminase 2. At the age of 4–5 weeks, Bcat2p.Q300*/p.Q300* mice displayed drastic increase of plasma levels of branch chain amino acids (BCAAs—leucine, isoleucine, valine) due to the incomplete catabolism of BCAAs, in addition to inducible arrhythmias ex vivo as well as cardiac conduction and repolarization disturbances. In line with these findings, plasma BCAA levels were positively correlated to electrocardiogram indices of conduction and repolarization in the German community-based KORA F4 Study. Isolated cardiomyocytes from Bcat2p.Q300*/p.Q300* mice revealed action potential (AP) prolongation, pro-arrhythmic events (early and late afterdepolarizations, triggered APs), and dysregulated calcium homeostasis. Incubation of human pluripotent stem cell-derived cardiomyocytes with elevated concentration of BCAAs induced similar calcium dysregulation and pro-arrhythmic events which were prevented by rapamycin, demonstrating the crucial involvement of mTOR pathway activation. Conclusions Our findings identify for the first time a causative link between elevated BCAAs and arrhythmia, which has implications for arrhythmogenesis in conditions associated with BCAA metabolism dysregulation such as diabetes, metabolic syndrome, and heart failure.
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Affiliation(s)
- Vincent Portero
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Thomas Nicol
- Mammalian genetics Unit, MRC Harwell Institute, Harwell, Oxfordshire, United Kingdom
| | - Svitlana Podliesna
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Gerard A Marchal
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Antonius Baartscheer
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Casini
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Rafik Tadros
- Cardiovascular Genetics Center, Montreal Heart Institute and Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Jorien L Treur
- Department of Psychiatry, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands
| | - Michael W T Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands
| | - I Jane Cox
- Institute for Hepatology London, Foundation for Liver Research, London, UK.,Faculty of Life Sciences & Medicine, Kings College, London, UK
| | - Fay Probert
- Department of Chemistry, University of Oxford, Oxford UK
| | - Tertius A Hough
- Mammalian genetics Unit, MRC Harwell Institute, Harwell, Oxfordshire, United Kingdom
| | - Sara Falcone
- Mammalian genetics Unit, MRC Harwell Institute, Harwell, Oxfordshire, United Kingdom
| | - Leander Beekman
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,IBE, Faculty of Medicine, Ludwig Maximilian's University (LMU) Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Gabi Kastenmüller
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Christian Gieger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Stefan Kääb
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilian's University (LMU) Munich, Germany.,German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Moritz F Sinner
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilian's University (LMU) Munich, Germany.,German Centre for Cardiovascular Research (DZHK), partner site: Munich Heart Alliance, Munich, Germany
| | - Andrew Blease
- Mammalian genetics Unit, MRC Harwell Institute, Harwell, Oxfordshire, United Kingdom
| | - Arie O Verkerk
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Connie R Bezzina
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Paul K Potter
- Mammalian genetics Unit, MRC Harwell Institute, Harwell, Oxfordshire, United Kingdom.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Carol Ann Remme
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
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5
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Haimson B, Meir O, Sudakevitz-Merzbach R, Elberg G, Friedrich S, Lovell PV, Paixão S, Klein R, Mello CV, Klar A. Natural loss of function of ephrin-B3 shapes spinal flight circuitry in birds. SCIENCE ADVANCES 2021; 7:7/24/eabg5968. [PMID: 34117069 PMCID: PMC8195482 DOI: 10.1126/sciadv.abg5968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/28/2021] [Indexed: 05/11/2023]
Abstract
Flight in birds evolved through patterning of the wings from forelimbs and transition from alternating gait to synchronous flapping. In mammals, the spinal midline guidance molecule ephrin-B3 instructs the wiring that enables limb alternation, and its deletion leads to synchronous hopping gait. Here, we show that the ephrin-B3 protein in birds lacks several motifs present in other vertebrates, diminishing its affinity for the EphA4 receptor. The avian ephrin-B3 gene lacks an enhancer that drives midline expression and is missing in galliforms. The morphology and wiring at brachial levels of the chicken embryonic spinal cord resemble those of ephrin-B3 null mice. Dorsal midline decussation, evident in the mutant mouse, is apparent at the chick brachial level and is prevented by expression of exogenous ephrin-B3 at the roof plate. Our findings support a role for loss of ephrin-B3 function in shaping the avian brachial spinal cord circuitry and facilitating synchronous wing flapping.
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Affiliation(s)
- Baruch Haimson
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Oren Meir
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Reut Sudakevitz-Merzbach
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Gerard Elberg
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Samantha Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Sónia Paixão
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rüdiger Klein
- Department Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA.
| | - Avihu Klar
- Department of Medical Neurobiology, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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6
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Carbone M, Arron ST, Beutler B, Bononi A, Cavenee W, Cleaver JE, Croce CM, D'Andrea A, Foulkes WD, Gaudino G, Groden JL, Henske EP, Hickson ID, Hwang PM, Kolodner RD, Mak TW, Malkin D, Monnat RJ, Novelli F, Pass HI, Petrini JH, Schmidt LS, Yang H. Tumour predisposition and cancer syndromes as models to study gene-environment interactions. Nat Rev Cancer 2020; 20:533-549. [PMID: 32472073 PMCID: PMC8104546 DOI: 10.1038/s41568-020-0265-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/18/2022]
Abstract
Cell division and organismal development are exquisitely orchestrated and regulated processes. The dysregulation of the molecular mechanisms underlying these processes may cause cancer, a consequence of cell-intrinsic and/or cell-extrinsic events. Cellular DNA can be damaged by spontaneous hydrolysis, reactive oxygen species, aberrant cellular metabolism or other perturbations that cause DNA damage. Moreover, several environmental factors may damage the DNA, alter cellular metabolism or affect the ability of cells to interact with their microenvironment. While some environmental factors are well established as carcinogens, there remains a large knowledge gap of others owing to the difficulty in identifying them because of the typically long interval between carcinogen exposure and cancer diagnosis. DNA damage increases in cells harbouring mutations that impair their ability to correctly repair the DNA. Tumour predisposition syndromes in which cancers arise at an accelerated rate and in different organs - the equivalent of a sensitized background - provide a unique opportunity to examine how gene-environment interactions influence cancer risk when the initiating genetic defect responsible for malignancy is known. Understanding the molecular processes that are altered by specific germline mutations, environmental exposures and related mechanisms that promote cancer will allow the design of novel and effective preventive and therapeutic strategies.
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Affiliation(s)
- Michele Carbone
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA.
| | - Sarah T Arron
- STA, JEC, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Beutler
- Center for Genetic Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Angela Bononi
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Webster Cavenee
- Ludwig Institute, University of California, San Diego, San Diego, CA, USA
| | - James E Cleaver
- STA, JEC, Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Ohio State University, Columbus, OH, USA
| | - Alan D'Andrea
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Giovanni Gaudino
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Elizabeth P Henske
- Center for LAM Research, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Paul M Hwang
- Cardiovascular Branch, National Institutes of Health, Bethesda, MD, USA
| | - Richard D Kolodner
- Ludwig Institute, University of California, San Diego, San Diego, CA, USA
| | - Tak W Mak
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - David Malkin
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Raymond J Monnat
- Department Pathology, Washington University, Seattle, WA, USA
- Department of Genome Science, Washington University, Seattle, WA, USA
| | - Flavia Novelli
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Harvey I Pass
- Department of Cardiovascular Surgery, New York University, New York, NY, USA
| | - John H Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Haining Yang
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI, USA
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7
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Hoyos-Manchado R, Villa-Consuegra S, Berraquero M, Jiménez J, Tallada VA. Mutational Analysis of N-Ethyl-N-Nitrosourea (ENU) in the Fission Yeast Schizosaccharomyces pombe. G3 (BETHESDA, MD.) 2020; 10:917-923. [PMID: 31900332 PMCID: PMC7056981 DOI: 10.1534/g3.119.400936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/31/2019] [Indexed: 12/04/2022]
Abstract
Forward genetics in model organisms has boosted our knowledge of the genetic bases of development, aging, and human diseases. In this experimental pipeline, it is crucial to start by inducing a large number of random mutations in the genome of the model organism to search for phenotypes of interest. Many chemical mutagens are used to this end because most of them display particular reactivity properties and act differently over DNA. Here we report the use of N-ethyl-N-nitrosourea (ENU) as a mutagen in the fission yeast Schizosaccharomyces pombe As opposed to many other alkylating agents, ENU only induces an S N 1-type reaction with a low s constant (s = 0.26), attacking preferentially O2 and O4 in thymine and O6 deoxyguanosine, leading to base substitutions rather than indels, which are extremely rare in its resulting mutagenic repertoire. Using ENU, we gathered a collection of 13 temperature-sensitive mutants and 80 auxotrophic mutants including two deleterious alleles of the human ortholog ATIC. Defective alleles of this gene cause AICA-ribosiduria, a severe genetic disease. In this screen, we also identified 13 aminoglycoside-resistance inactivating mutations in APH genes. Mutations reported here may be of interest for metabolism related diseases and antibiotic resistance research fields.
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Affiliation(s)
- Rafael Hoyos-Manchado
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Carretera de Utrera Km1, 41013 Seville, Spain
| | - Sergio Villa-Consuegra
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Carretera de Utrera Km1, 41013 Seville, Spain
| | - Modesto Berraquero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Carretera de Utrera Km1, 41013 Seville, Spain
| | - Juan Jiménez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Carretera de Utrera Km1, 41013 Seville, Spain
| | - Víctor A Tallada
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas, Carretera de Utrera Km1, 41013 Seville, Spain
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8
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McAlpine W, Russell J, Murray AR, Beutler B, Turer E. Research Techniques Made Simple: Forward Genetic Screening to Uncover Genes Involved in Skin Biology. J Invest Dermatol 2019; 139:1848-1853.e1. [PMID: 31445571 DOI: 10.1016/j.jid.2019.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022]
Abstract
The primary goals of modern genetics are to identify disease-causing mutations and to define the functions of genes in biological processes. Two complementary approaches, reverse and forward genetics, can be used to achieve this goal. Reverse genetics is a gene-driven approach that comprises specific gene targeting followed by phenotypic assessment. Conversely, forward genetics is a phenotype-driven approach that involves the phenotypic screening of organisms with randomly induced mutations followed by subsequent identification of the causative mutations (i.e., those responsible for phenotype). In this article, we focus on how forward genetics in mice can be used to explore dermatologic disease. We outline mouse mutagenesis with the chemical N-ethyl-N-nitrosourea and the strategy used to instantaneously identify mutations that are causative of specific phenotypes. Furthermore, we summarize the types of phenotypic screens that can be performed to explore various aspects of dermatologic disease.
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Affiliation(s)
- William McAlpine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Emre Turer
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
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9
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Brommage R, Powell DR, Vogel P. Predicting human disease mutations and identifying drug targets from mouse gene knockout phenotyping campaigns. Dis Model Mech 2019; 12:dmm038224. [PMID: 31064765 PMCID: PMC6550044 DOI: 10.1242/dmm.038224] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two large-scale mouse gene knockout phenotyping campaigns have provided extensive data on the functions of thousands of mammalian genes. The ongoing International Mouse Phenotyping Consortium (IMPC), with the goal of examining all ∼20,000 mouse genes, has examined 5115 genes since 2011, and phenotypic data from several analyses are available on the IMPC website (www.mousephenotype.org). Mutant mice having at least one human genetic disease-associated phenotype are available for 185 IMPC genes. Lexicon Pharmaceuticals' Genome5000™ campaign performed similar analyses between 2000 and the end of 2008 focusing on the druggable genome, including enzymes, receptors, transporters, channels and secreted proteins. Mutants (4654 genes, with 3762 viable adult homozygous lines) with therapeutically interesting phenotypes were studied extensively. Importantly, phenotypes for 29 Lexicon mouse gene knockouts were published prior to observations of similar phenotypes resulting from homologous mutations in human genetic disorders. Knockout mouse phenotypes for an additional 30 genes mimicked previously published human genetic disorders. Several of these models have helped develop effective treatments for human diseases. For example, studying Tph1 knockout mice (lacking peripheral serotonin) aided the development of telotristat ethyl, an approved treatment for carcinoid syndrome. Sglt1 (also known as Slc5a1) and Sglt2 (also known as Slc5a2) knockout mice were employed to develop sotagliflozin, a dual SGLT1/SGLT2 inhibitor having success in clinical trials for diabetes. Clinical trials evaluating inhibitors of AAK1 (neuropathic pain) and SGLT1 (diabetes) are underway. The research community can take advantage of these unbiased analyses of gene function in mice, including the minimally studied 'ignorome' genes.
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Affiliation(s)
- Robert Brommage
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - David R Powell
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - Peter Vogel
- St. Jude Children's Research Hospital, Pathology, MS 250, Room C5036A, 262 Danny Thomas Place, Memphis, TN 38105, USA
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10
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Tomberg K, Westrick RJ, Kotnik EN, Cleuren AC, Siemieniak DR, Zhu G, Saunders TL, Ginsburg D. Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse. PLoS Genet 2018; 14:e1007658. [PMID: 30188893 PMCID: PMC6143275 DOI: 10.1371/journal.pgen.1007658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/18/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
Although the Factor V Leiden (FVL) gene variant is the most prevalent genetic risk factor for venous thrombosis, only 10% of FVL carriers will experience such an event in their lifetime. To identify potential FVL modifier genes contributing to this incomplete penetrance, we took advantage of a perinatal synthetic lethal thrombosis phenotype in mice homozygous for FVL (F5L/L) and haploinsufficient for tissue factor pathway inhibitor (Tfpi+/-) to perform a sensitized dominant ENU mutagenesis screen. Linkage analysis conducted in the 3 largest pedigrees generated from the surviving F5L/L Tfpi+/- mice ('rescues') using ENU-induced coding variants as genetic markers was unsuccessful in identifying major suppressor loci. Whole exome sequencing was applied to DNA from 107 rescue mice to identify candidate genes enriched for ENU mutations. A total of 3,481 potentially deleterious candidate ENU variants were identified in 2,984 genes. After correcting for gene size and multiple testing, Arl6ip5 was identified as the most enriched gene, though not reaching genome-wide significance. Evaluation of CRISPR/Cas9 induced loss of function in the top 6 genes failed to demonstrate a clear rescue phenotype. However, a maternally inherited (not ENU-induced) de novo mutation (Plcb4R335Q) exhibited significant co-segregation with the rescue phenotype (p = 0.003) in the corresponding pedigree. Thrombosis suppression by heterozygous Plcb4 loss of function was confirmed through analysis of an independent, CRISPR/Cas9-induced Plcb4 mutation (p = 0.01).
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Affiliation(s)
- Kärt Tomberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Randal J. Westrick
- Department of Biological Sciences and Center for Data Science and Big Data Analysis, Oakland University, Rochester, Michigan, United States of America
| | - Emilee N. Kotnik
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Audrey C. Cleuren
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R Siemieniak
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas L. Saunders
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Transgenic Animal Model Core Laboratory, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David Ginsburg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Internal Medicine, Division of Molecular Medicine and Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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11
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Blease A, Nicol T, Falcone S, Starbuck B, Greenaway S, Hutchinson M, Potter PK. Generation and Identification of Mutations Resulting in Chronic and Age-Related Phenotypes in Mice. ACTA ACUST UNITED AC 2018; 8:e42. [PMID: 29927552 DOI: 10.1002/cpmo.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aging is inevitable, and our society must deal with the consequences: namely, an increased incidence of disease and ill health. Many mouse models of disease are acute or early onset or are induced in young mice, despite the fact that aging is a significant risk factor for a range of significant diseases. To improve modeling of such diseases, we should incorporate aging into our models. Many systems are affected by aging, with a decline in mitochondrial function, an increase in senescence, a loss of resilience, telomere shortening, and a decline in immune function being key factors in the increased susceptibility to disease that is associated with aging. To develop novel models of age-related disease, we undertook a phenotype-driven screen of a pipeline of mutagenized mice. Here, we describe some of the underlying protocols and outline important aspects to consider when studying aged mice. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Andrew Blease
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Thomas Nicol
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Sara Falcone
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Becky Starbuck
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Simon Greenaway
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Marie Hutchinson
- Mary Lyon Centre, Medical Research Council Harwell Science and Innovation Campus, Oxford, United Kingdom
| | - Paul K Potter
- Mammalian Genetics Unit, Medical Research Council, Harwell Science and Innovation Campus, Oxford, United Kingdom
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12
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Unpackaging the genetics of mammalian fertility: strategies to identify the “reproductive genome”†. Biol Reprod 2018; 99:1119-1128. [DOI: 10.1093/biolre/ioy133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/05/2018] [Indexed: 12/18/2022] Open
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13
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Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells S. High-throughput mouse phenomics for characterizing mammalian gene function. Nat Rev Genet 2018; 19:357-370. [PMID: 29626206 PMCID: PMC6582361 DOI: 10.1038/s41576-018-0005-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We are entering a new era of mouse phenomics, driven by large-scale and economical generation of mouse mutants coupled with increasingly sophisticated and comprehensive phenotyping. These studies are generating large, multidimensional gene-phenotype data sets, which are shedding new light on the mammalian genome landscape and revealing many hitherto unknown features of mammalian gene function. Moreover, these phenome resources provide a wealth of disease models and can be integrated with human genomics data as a powerful approach for the interpretation of human genetic variation and its relationship to disease. In the future, the development of novel phenotyping platforms allied to improved computational approaches, including machine learning, for the analysis of phenotype data will continue to enhance our ability to develop a comprehensive and powerful model of mammalian gene-phenotype space.
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Affiliation(s)
| | - Chris C Holmes
- Nuffield Department of Medicine and Department of Statistics, University of Oxford, Oxford, UK.
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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14
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Revollo JR, Dad A, McDaniel LP, Pearce MG, Dobrovolsky VN. Genome-wide mutation detection by interclonal genetic variation. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 829-830:61-69. [PMID: 29704995 DOI: 10.1016/j.mrgentox.2018.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/10/2018] [Accepted: 03/10/2018] [Indexed: 12/20/2022]
Abstract
Genetic toxicology assays estimate mutation frequencies by phenotypically screening for the activation or inactivation of endogenous or exogenous reporter genes. These reporters can only detect mutations in narrow areas of the genome and their use is often restricted to certain in vitro and in vivo models. Here, we show that Interclonal Genetic Variation (ICGV) can directly identify mutations genome-wide by comparing sequencing data of single-cell clones derived from the same source or organism. Upon ethyl methanesulfonate (EMS) exposure, ICGV detected greater levels of mutation in a dose- and time-dependent manner in E. coli. In addition, ICGV was also able to identify a ∼20-fold increase in somatic mutations in T-cell clones derived from an N-ethyl-N-nitrosourea (ENU)-treated rat vs. a vehicle-treated rat. These results demonstrate that the genetic differences of single-cell clones can be used for genome-wide mutation detection.
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Affiliation(s)
- Javier R Revollo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA.
| | - Azra Dad
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Lea P McDaniel
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Mason G Pearce
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
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15
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An ENU-induced splice site mutation of mouse Col1a1 causing recessive osteogenesis imperfecta and revealing a novel splicing rescue. Sci Rep 2017; 7:11717. [PMID: 28916811 PMCID: PMC5600972 DOI: 10.1038/s41598-017-10343-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/02/2017] [Indexed: 02/06/2023] Open
Abstract
GU-AG consensus sequences are used for intron recognition in the majority of cases of pre-mRNA splicing in eukaryotes. Mutations at splice junctions often cause exon skipping, short deletions, or insertions in the mature mRNA, underlying one common molecular mechanism of genetic diseases. Using N-ethyl-N-nitrosourea, a novel recessive mutation named seal was produced, associated with fragile bones and susceptibility to fractures (spine and limbs). A single nucleotide transversion (T → A) at the second position of intron 36 of the Col1a1 gene, encoding the type I collagen, α1 chain, was responsible for the phenotype. Col1a1 seal mRNA expression occurred at greatly reduced levels compared to the wild-type transcript, resulting in reduced and aberrant collagen fibers in tibiae of seal homozygous mice. Unexpectedly, splicing of Col1a1 seal mRNA followed the normal pattern despite the presence of the donor splice site mutation, likely due to the action of a putative intronic splicing enhancer present in intron 25, which appeared to function redundantly with the splice donor site of intron 36. Seal mice represent a model of human osteogenesis imperfecta, and reveal a previously unknown mechanism for splicing "rescue."
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16
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Eppig JT. Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse. ILAR J 2017; 58:17-41. [PMID: 28838066 PMCID: PMC5886341 DOI: 10.1093/ilar/ilx013] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 03/14/2017] [Accepted: 03/28/2017] [Indexed: 12/13/2022] Open
Abstract
The Mouse Genome Informatics (MGI) Resource supports basic, translational, and computational research by providing high-quality, integrated data on the genetics, genomics, and biology of the laboratory mouse. MGI serves a strategic role for the scientific community in facilitating biomedical, experimental, and computational studies investigating the genetics and processes of diseases and enabling the development and testing of new disease models and therapeutic interventions. This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings of MGI. MGI develops and maintains a gold-standard resource that reflects the current state of knowledge, provides semantic and contextual data integration that fosters hypothesis testing, continually develops new and improved tools for searching and analysis, and partners with the scientific community to assure research data needs are met. Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data. References and links to additional MGI aspects are provided.
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Affiliation(s)
- Janan T. Eppig
- Janan T. Eppig, PhD, is Professor Emeritus at The Jackson Laboratory in Bar Harbor, Maine
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17
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Gallego-Llamas J, Timms AE, Pitstick R, Peters J, Carlson GA, Beier DR. Improvement of ENU Mutagenesis Efficiency Using Serial Injection and Mismatch Repair Deficiency Mice. PLoS One 2016; 11:e0159377. [PMID: 27441645 PMCID: PMC4956170 DOI: 10.1371/journal.pone.0159377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 12/05/2022] Open
Abstract
ENU mutagenesis is a powerful method for generating novel lines of mice that are informative with respect to both fundamental biological processes and human disease. Rapid developments in genomic technology have made the task of identifying causal mutations by positional cloning remarkably efficient. One limitation of this approach remains the mutation frequency achievable using standard treatment protocols, which currently generate approximately 1–2 sequence changes per megabase when optimized. In this study we used two strategies to attempt to increase the number of mutations induced by ENU treatment. One approach employed mice carrying a mutation in the DNA repair enzyme Msh6. The second strategy involved injection of ENU to successive generations of mice. To evaluate the number of ENU-induced mutations, single mice or pooled samples were analyzed using whole exome sequencing. The results showed that there is considerable variability in the induced mutation frequency using these approaches, but an overall increase in ENU-induced variants from one generation to another was observed. The analysis of the mice deficient for Msh6 also showed an increase in the ENU-induced variants compared to the wild-type ENU-treated mice. However, in both cases the increase in ENU-induced mutation frequency was modest.
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Affiliation(s)
- Jabier Gallego-Llamas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Andrew E. Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Rose Pitstick
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - Janet Peters
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - George A. Carlson
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
- * E-mail:
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18
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Mutation of Fnip1 is associated with B-cell deficiency, cardiomyopathy, and elevated AMPK activity. Proc Natl Acad Sci U S A 2016; 113:E3706-15. [PMID: 27303042 DOI: 10.1073/pnas.1607592113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Folliculin (FLCN) is a tumor-suppressor protein mutated in the Birt-Hogg-Dubé (BHD) syndrome, which associates with two paralogous proteins, folliculin-interacting protein (FNIP)1 and FNIP2, forming a complex that interacts with the AMP-activated protein kinase (AMPK). Although it is clear that this complex influences AMPK and other metabolic regulators, reports of its effects have been inconsistent. To address this issue, we created a recessive loss-of-function variant of Fnip1 Homozygous FNIP1 deficiency resulted in profound B-cell deficiency, partially restored by overexpression of the antiapoptotic protein BCL2, whereas heterozygous deficiency caused a loss of marginal zone B cells. FNIP1-deficient mice developed cardiomyopathy characterized by left ventricular hypertrophy and glycogen accumulation, with close parallels to mice and humans bearing gain-of-function mutations in the γ2 subunit of AMPK. Concordantly, γ2-specific AMPK activity was elevated in neonatal FNIP1-deficient myocardium, whereas AMPK-dependent unc-51-like autophagy activating kinase 1 (ULK1) phosphorylation and autophagy were increased in FNIP1-deficient B-cell progenitors. These data support a role for FNIP1 as a negative regulator of AMPK.
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19
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Keller RR, Gestl SA, Lu AQ, Hoke A, Feith DJ, Gunther EJ. Carcinogen-specific mutations in preferred Ras-Raf pathway oncogenes directed by strand bias. Carcinogenesis 2016; 37:810-816. [PMID: 27207659 PMCID: PMC4967214 DOI: 10.1093/carcin/bgw061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/07/2016] [Indexed: 12/24/2022] Open
Abstract
Carcinogen exposures inscribe mutation patterns on cancer genomes and sometimes bias the acquisition of driver mutations toward preferred oncogenes, potentially dictating sensitivity to targeted agents. Whether and how carcinogen-specific mutation patterns direct activation of preferred oncogenes remains poorly understood. Here, mouse models of breast cancer were exploited to uncover a mechanistic link between strand-biased mutagenesis and oncogene preference. When chemical carcinogens were employed during Wnt1-initiated mammary tumorigenesis, exposure to either 7,12-dimethylbenz(a)anthracene (DMBA) or N-ethyl-N-nitrosourea (ENU) dramatically accelerated tumor onset. Mammary tumors that followed DMBA exposure nearly always activated the Ras pathway via somatic Hras(CAA61CTA) mutations. Surprisingly, mammary tumors that followed ENU exposure typically lacked Hras mutations, and instead activated the Ras pathway downstream via Braf(GTG636GAG) mutations. Hras(CAA61CTA) mutations involve an A-to-T change on the sense strand, whereas Braf(GTG636GAG) mutations involve an inverse T-to-A change, suggesting that strand-biased mutagenesis may determine oncogene preference. To examine this possibility further, we turned to an alternative Wnt-driven tumor model in which carcinogen exposures augment a latent mammary tumor predisposition in Apc(min) mice. DMBA and ENU each accelerated mammary tumor onset in Apc(min) mice by introducing somatic, "second-hit" Apc mutations. Consistent with our strand bias model, DMBA and ENU generated strikingly distinct Apc mutation patterns, including stringently strand-inverse mutation signatures at A:T sites. Crucially, these contrasting signatures precisely match those proposed to confer bias toward Hras(CAA61CTA) versus Braf(GTG636GAG) mutations in the original tumor sets. Our findings highlight a novel mechanism whereby exposure history acts through strand-biased mutagenesis to specify activation of preferred oncogenes.
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Affiliation(s)
- Ross R Keller
- Jake Gittlen Laboratories for Cancer Research and.,Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Shelley A Gestl
- Jake Gittlen Laboratories for Cancer Research and.,Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Amy Q Lu
- Jake Gittlen Laboratories for Cancer Research and.,Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Alicia Hoke
- Jake Gittlen Laboratories for Cancer Research and.,Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - David J Feith
- Division of Hematology and the Cancer Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA and
| | - Edward J Gunther
- Jake Gittlen Laboratories for Cancer Research and.,Penn State Hershey Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Medicine (Hematology/Oncology), Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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20
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Morin MD, Wang Y, Jones BT, Su L, Surakattula MMRP, Berger M, Huang H, Beutler EK, Zhang H, Beutler B, Boger DL. Discovery and Structure-Activity Relationships of the Neoseptins: A New Class of Toll-like Receptor-4 (TLR4) Agonists. J Med Chem 2016; 59:4812-30. [PMID: 27050713 DOI: 10.1021/acs.jmedchem.6b00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we report studies leading to the discovery of the neoseptins and a comprehensive examination of the structure-activity relationships (SARs) of this new class of small-molecule mouse Toll-like receptor 4 (mTLR4) agonists. The compounds in this class, which emerged from screening an α-helix mimetic library, stimulate the immune response, act by a well-defined mechanism (mouse TLR4 agonist), are easy to produce and structurally manipulate, exhibit exquisite SARs, are nontoxic, and elicit improved and qualitatively different responses compared to lipopolysaccharide, even though they share the same receptor.
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Affiliation(s)
- Matthew D Morin
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ying Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Brian T Jones
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lijing Su
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Murali M R P Surakattula
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael Berger
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hua Huang
- Department of Genetics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Elliot K Beutler
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hong Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Dale L Boger
- Department of Chemistry and the Skaggs Institute of Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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21
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Simon MM, Moresco EMY, Bull KR, Kumar S, Mallon AM, Beutler B, Potter PK. Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. Mamm Genome 2015; 26:486-500. [PMID: 26449678 PMCID: PMC4602060 DOI: 10.1007/s00335-015-9603-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/01/2015] [Indexed: 02/07/2023]
Abstract
Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to ‘finding a needle in a haystack’. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation.
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Affiliation(s)
- Michelle M Simon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine R Bull
- Nuffield Department of Medicine and Wellcome Trust Centre for Human Genetics, Oxford University, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Saumya Kumar
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Paul K Potter
- Medical Research Council Harwell (Mammalian Genetics Unit and Mary Lyon Centre), Harwell Campus, Oxfordshire, OX11 0RD, UK
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22
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Mutation of the ER retention receptor KDELR1 leads to cell-intrinsic lymphopenia and a failure to control chronic viral infection. Proc Natl Acad Sci U S A 2015; 112:E5706-14. [PMID: 26438836 DOI: 10.1073/pnas.1515619112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endoplasmic reticulum (ER)-resident proteins are continually retrieved from the Golgi and returned to the ER by Lys-Asp-Glu-Leu (KDEL) receptors, which bind to an eponymous tetrapeptide motif at their substrate's C terminus. Mice and humans possess three paralogous KDEL receptors, but little is known about their functional redundancy, or if their mutation can be physiologically tolerated. Here, we present a recessive mouse missense allele of the prototypical mammalian KDEL receptor, KDEL ER protein retention receptor 1 (KDELR1). Kdelr1 homozygous mutants were mildly lymphopenic, as were mice with a CRISPR/Cas9-engineered frameshift allele. Lymphopenia was cell intrinsic and, in the case of T cells, was associated with reduced expression of the T-cell receptor (TCR) and increased expression of CD44, and could be partially corrected by an MHC class I-restricted TCR transgene. Antiviral immunity was also compromised, with Kdelr1 mutant mice unable to clear an otherwise self-limiting viral infection. These data reveal a nonredundant cellular function for KDELR1, upon which lymphocytes distinctly depend.
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Eppig JT, Motenko H, Richardson JE, Richards-Smith B, Smith CL. The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources. Mamm Genome 2015; 26:448-55. [PMID: 26373861 PMCID: PMC4602064 DOI: 10.1007/s00335-015-9600-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/10/2015] [Indexed: 11/04/2022]
Abstract
The availability of and access to quality genetically defined, health-status known mouse resources is critical for biomedical research. By ensuring that mice used in research experiments are biologically, genetically, and health-status equivalent, we enable knowledge transfer, hypothesis building based on multiple data streams, and experimental reproducibility based on common mouse resources (reagents). Major repositories for mouse resources have developed over time and each has significant unique resources to offer. Here we (a) describe The International Mouse Strain Resource that offers users a combined catalog of worldwide mouse resources (live, cryopreserved, embryonic stem cells), with direct access to repository sites holding resources of interest and (b) discuss the commitment to nomenclature standards among resources that remain a challenge in unifying mouse resource catalogs.
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Affiliation(s)
- Janan T Eppig
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
| | - Howie Motenko
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
| | - Joel E Richardson
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
| | | | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA.
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Eppig JT, Richardson JE, Kadin JA, Ringwald M, Blake JA, Bult CJ. Mouse Genome Informatics (MGI): reflecting on 25 years. Mamm Genome 2015; 26:272-84. [PMID: 26238262 PMCID: PMC4534491 DOI: 10.1007/s00335-015-9589-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 12/02/2022]
Abstract
From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human health and disease. This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips. Through major paradigm shifts in biological research and computer technologies, MGI has adapted and evolved to become an integral part of the larger global bioinformatics infrastructure and honed its ability to provide authoritative reference datasets used and incorporated by many other established bioinformatics resources. Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner.
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Affiliation(s)
- Janan T. Eppig
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Joel E. Richardson
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - James A. Kadin
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Martin Ringwald
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Judith A. Blake
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Carol J. Bult
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609 USA
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Siggs OM, Miosge LA, Daley SR, Asquith K, Foster PS, Liston A, Goodnow CC. Quantitative reduction of the TCR adapter protein SLP-76 unbalances immunity and immune regulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:2587-95. [PMID: 25662996 PMCID: PMC4355390 DOI: 10.4049/jimmunol.1400326] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gene variants that disrupt TCR signaling can cause severe immune deficiency, yet less disruptive variants are sometimes associated with immune pathology. Null mutations of the gene encoding the scaffold protein Src homology 2 domain-containing leukocyte protein of 76 kDa (SLP-76), for example, cause an arrest of T cell positive selection, whereas a synthetic membrane-targeted allele allows limited positive selection but is associated with proinflammatory cytokine production and autoantibodies. Whether these and other enigmatic outcomes are due to a biochemical uncoupling of tolerogenic signaling, or simply a quantitative reduction of protein activity, remains to be determined. In this study we describe a splice variant of Lcp2 that reduced the amount of wild-type SLP-76 protein by ~90%, disrupting immunogenic and tolerogenic pathways to different degrees. Mutant mice produced excessive amounts of proinflammatory cytokines, autoantibodies, and IgE, revealing that simple quantitative reductions of SLP-76 were sufficient to trigger immune dysregulation. This allele reveals a dose-sensitive threshold for SLP-76 in the balance of immunity and immune dysregulation, a common disturbance of atypical clinical immune deficiencies.
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Affiliation(s)
- Owen M Siggs
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
| | - Lisa A Miosge
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Stephen R Daley
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Kelly Asquith
- Priority Research Centre for Asthma and Respiratory Diseases, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales 2300, Australia; and
| | - Paul S Foster
- Priority Research Centre for Asthma and Respiratory Diseases, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales 2300, Australia; and
| | - Adrian Liston
- Department of Microbiology and Immunology, Flanders Institute for Biotechnology and University of Leuven, Leuven 3000, Belgium
| | - Christopher C Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia;
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Abstract
With the wide availability of massively parallel sequencing technologies, genetic mapping has become the rate limiting step in mammalian forward genetics. Here we introduce a method for real-time identification of N-ethyl-N-nitrosourea-induced mutations that cause phenotypes in mice. All mutations are identified by whole exome G1 progenitor sequencing and their zygosity is established in G2/G3 mice before phenotypic assessment. Quantitative and qualitative traits, including lethal effects, in single or multiple combined pedigrees are then analyzed with Linkage Analyzer, a software program that detects significant linkage between individual mutations and aberrant phenotypic scores and presents processed data as Manhattan plots. As multiple alleles of genes are acquired through mutagenesis, pooled "superpedigrees" are created to analyze the effects. Our method is distinguished from conventional forward genetic methods because it permits (1) unbiased declaration of mappable phenotypes, including those that are incompletely penetrant (2), automated identification of causative mutations concurrent with phenotypic screening, without the need to outcross mutant mice to another strain and backcross them, and (3) exclusion of genes not involved in phenotypes of interest. We validated our approach and Linkage Analyzer for the identification of 47 mutations in 45 previously known genes causative for adaptive immune phenotypes; our analysis also implicated 474 genes not previously associated with immune function. The method described here permits forward genetic analysis in mice, limited only by the rates of mutant production and screening.
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Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E. An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol 2015; 14:R96. [PMID: 24025402 PMCID: PMC4053835 DOI: 10.1186/gb-2013-14-9-r96] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/06/2013] [Indexed: 12/28/2022] Open
Abstract
Background We have used a sensitized ENU mutagenesis screen to produce mouse lines that carry mutations in genes required for epigenetic regulation. We call these lines Modifiers of murine metastable epialleles (Mommes). Results We report a basic molecular and phenotypic characterization for twenty of the Momme mouse lines, and in each case we also identify the causative mutation. Three of the lines carry a mutation in a novel epigenetic modifier, Rearranged L-myc fusion (Rlf), and one gene, Rap-interacting factor 1 (Rif1), has not previously been reported to be involved in transcriptional regulation in mammals. Many of the other lines are novel alleles of known epigenetic regulators. For two genes, Rlf and Widely-interspaced zinc finger (Wiz), we describe the first mouse mutants. All of the Momme mutants show some degree of homozygous embryonic lethality, emphasizing the importance of epigenetic processes. The penetrance of lethality is incomplete in a number of cases. Similarly, abnormalities in phenotype seen in the heterozygous individuals of some lines occur with incomplete penetrance. Conclusions Recent advances in sequencing enhance the power of sensitized mutagenesis screens to identify the function of previously uncharacterized factors and to discover additional functions for previously characterized proteins. The observation of incomplete penetrance of phenotypes in these inbred mutant mice, at various stages of development, is of interest. Overall, the Momme collection of mouse mutants provides a valuable resource for researchers across many disciplines.
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Arime Y, Fukumura R, Miura I, Mekada K, Yoshiki A, Wakana S, Gondo Y, Akiyama K. Effects of background mutations and single nucleotide polymorphisms (SNPs) on the Disc1 L100P behavioral phenotype associated with schizophrenia in mice. Behav Brain Funct 2014; 10:45. [PMID: 25487992 PMCID: PMC4295473 DOI: 10.1186/1744-9081-10-45] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/21/2014] [Indexed: 01/31/2023] Open
Abstract
Background Disrupted-in-schizophrenia 1 (DISC1) is a promising candidate susceptibility gene for psychiatric disorders, including schizophrenia, bipolar disorder and major depression. Several previous studies reported that mice with N-ethyl-N-nitrosourea (ENU)-induced L100P mutation in Disc1 showed some schizophrenia-related behavioral phenotypes. This line originally carried several thousands of ENU-induced point mutations in the C57BL/6 J strain and single nucleotide polymorphisms (SNPs) from the DBA/2 J inbred strain. Methods To investigate the effect of Disc1 L100P, background mutations and SNPs on phenotypic characterization, we performed behavioral analyses to better understand phenotypes of Disc1 L100P mice and comprehensive genetic analyses using whole-exome resequencing and SNP panels to map ENU-induced mutations and strain-specific SNPs, respectively. Results We found no differences in spontaneous or methamphetamine-induced locomotor activity, sociability or social novelty preference among Disc1 L100P/L100P, L100P/+ mutants and wild-type littermates. Whole-exome resequencing of the original G1 mouse identified 117 ENU-induced variants, including Disc1 L100P per se. Two females and three males from the congenic L100P strain after backcrossing to C57BL/6 J were deposited to RIKEN BioResource Center in 2008. We genotyped them with DBA/2 J × C57BL/6 J SNPs and found a number of the checked SNPs still remained. Conclusion These results suggest that causal attribution of the discrepancy in behavioral phenotypes to the Disc1 L100P mutant mouse line existing among different research groups needs to be cautiously investigated in further study by taking into account the effect(s) of other ENU-induced mutations and/or SNPs from DBA/2 J. Electronic supplementary material The online version of this article (doi:10.1186/1744-9081-10-45) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Kazufumi Akiyama
- Department of Biological Psychiatry and Neuroscience, Dokkyo Medical University School of Medicine, 800 Kitakobayashi, Mibu-machi, Shimotsuga-gun, Tochigi 321-0293, Japan.
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Tokunaga M, Kokubu C, Maeda Y, Sese J, Horie K, Sugimoto N, Kinoshita T, Yusa K, Takeda J. Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. BMC Genomics 2014; 15:1016. [PMID: 25418962 PMCID: PMC4301880 DOI: 10.1186/1471-2164-15-1016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 11/12/2014] [Indexed: 12/04/2022] Open
Abstract
Background Genome-wide saturation mutagenesis and subsequent phenotype-driven screening has been central to a comprehensive understanding of complex biological processes in classical model organisms such as flies, nematodes, and plants. The degree of “saturation” (i.e., the fraction of possible target genes identified) has been shown to be a critical parameter in determining all relevant genes involved in a biological function, without prior knowledge of their products. In mammalian model systems, however, the relatively large scale and labor intensity of experiments have hampered the achievement of actual saturation mutagenesis, especially for recessive traits that require biallelic mutations to manifest detectable phenotypes. Results By exploiting the recently established haploid mouse embryonic stem cells (ESCs), we present an implementation of almost complete saturation mutagenesis in a mammalian system. The haploid ESCs were mutagenized with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and processed for the screening of mutants defective in various steps of the glycosylphosphatidylinositol-anchor biosynthetic pathway. The resulting 114 independent mutant clones were characterized by a functional complementation assay, and were shown to be defective in any of 20 genes among all 22 known genes essential for this well-characterized pathway. Ten mutants were further validated by whole-exome sequencing. The predominant generation of single-nucleotide substitutions by ENU resulted in a gene mutation rate proportional to the length of the coding sequence, which facilitated the experimental design of saturation mutagenesis screening with the aid of computational simulation. Conclusions Our study enables mammalian saturation mutagenesis to become a realistic proposition. Computational simulation, combined with a pilot mutagenesis experiment, could serve as a tool for the estimation of the number of genes essential for biological processes such as drug target pathways when a positive selection of mutants is available. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1016) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Kosuke Yusa
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
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Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res 2014; 43:D726-36. [PMID: 25348401 PMCID: PMC4384027 DOI: 10.1093/nar/gku967] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse–human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human–Mouse: Disease Connection, allows users to explore gene–phenotype–disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community.
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Affiliation(s)
- Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Judith A Blake
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives. Genes (Basel) 2014; 5:887-925. [PMID: 25268389 PMCID: PMC4276919 DOI: 10.3390/genes5040887] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/19/2014] [Accepted: 08/21/2014] [Indexed: 12/30/2022] Open
Abstract
Infectious diseases are responsible for over 25% of deaths globally, but many more individuals are exposed to deadly pathogens. The outcome of infection results from a set of diverse factors including pathogen virulence factors, the environment, and the genetic make-up of the host. The completion of the human reference genome sequence in 2004 along with technological advances have tremendously accelerated and renovated the tools to study the genetic etiology of infectious diseases in humans and its best characterized mammalian model, the mouse. Advancements in mouse genomic resources have accelerated genome-wide functional approaches, such as gene-driven and phenotype-driven mutagenesis, bringing to the fore the use of mouse models that reproduce accurately many aspects of the pathogenesis of human infectious diseases. Treatment with the mutagen N-ethyl-N-nitrosourea (ENU) has become the most popular phenotype-driven approach. Our team and others have employed mouse ENU mutagenesis to identify host genes that directly impact susceptibility to pathogens of global significance. In this review, we first describe the strategies and tools used in mouse genetics to understand immunity to infection with special emphasis on chemical mutagenesis of the mouse germ-line together with current strategies to efficiently identify functional mutations using next generation sequencing. Then, we highlight illustrative examples of genes, proteins, and cellular signatures that have been revealed by ENU screens and have been shown to be involved in susceptibility or resistance to infectious diseases caused by parasites, bacteria, and viruses.
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32
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Siggs OM. Dissecting mammalian immunity through mutation. Immunol Cell Biol 2014; 92:392-9. [PMID: 24518983 PMCID: PMC4038135 DOI: 10.1038/icb.2014.8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/15/2014] [Accepted: 01/15/2014] [Indexed: 12/27/2022]
Abstract
Although mutation and natural selection have given rise to our immune system, a well-placed mutation can also cripple it, and within an expanding population we are recognizing more and more cases of single-gene mutations that compromise immunity. These mutations are an ideal tool for understanding human immunology, and there are more ways than ever to measure their physiological effects. There are also more ways to create mutations in the laboratory, and to use these resources to systematically define the function of every gene in our genome. This review focuses on the discovery and creation of mutations in the context of mammalian immunity, with an emphasis on the use of genome-wide chemical and CRISPR/Cas9 mutagenesis to reveal gene function.
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Affiliation(s)
- Owen M Siggs
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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33
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Moresco EMY, Li X, Beutler B. Going forward with genetics: recent technological advances and forward genetics in mice. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 182:1462-73. [PMID: 23608223 DOI: 10.1016/j.ajpath.2013.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 02/05/2013] [Indexed: 12/24/2022]
Abstract
Forward genetic analysis is an unbiased approach for identifying genes essential to defined biological phenomena. When applied to mice, it is one of the most powerful methods to facilitate understanding of the genetic basis of human biology and disease. The speed at which disease-causing mutations can be identified in mutagenized mice has been markedly increased by recent advances in DNA sequencing technology. Creating and analyzing mutant phenotypes may therefore become rate-limiting in forward genetic experimentation. We review the forward genetic approach and its future in the context of recent technological advances, in particular massively parallel DNA sequencing, induced pluripotent stem cells, and haploid embryonic stem cells.
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Affiliation(s)
- Eva Marie Y Moresco
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75235-8505, USA
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Edderkaoui B, Kesavan C, Baylink DJ, Wergedal JE, Srivastava AK, Mohan S. ENU mutation mapped to a distal region of chromosome 11 is a major determinant of bone size. Physiol Genomics 2013; 45:1222-8. [PMID: 24151243 DOI: 10.1152/physiolgenomics.00142.2013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Using a phenotype driven n-ethyl-nitrosourea (ENU) screen in growth hormone-deficient mice, we have identified a mutant (named 14104) that exhibited a smaller bone size. Phenotype measurements by microcomputed tomography revealed that mutant mice exhibited a 43 and 34% reduction in tissue area and bone area, respectively at the femur middiaphysis. Dynamic histomorphometry revealed a 30 and 15% lower bone formation rate at the periosteal and endosteal surface, respectively. Breaking strength of the femur was reduced by 30% in the mutant mice. To determine if the 14104 locus is involved in a mechanical loading signaling pathway, the skeletal anabolic response to tibia axial loading was evaluated. The increase in trabecular response in the loaded region was severely compromised by the 14014 mutation. To identify the location of mutation, we performed linkage analysis using 62 polymorphic markers in the B6-DBA/2J F2 mice. The genome-wide linkage analysis identified the location of the mutation to a 72 to 83 cM region on chromosome 11 with peak logarithm of the odds scores of 15 for periosteal circumference at marker D11mit338. Sequence analysis revealed no mutation in the coding region of 11 potential candidate genes. Based on these data and published data on the skeletal phenotype of genes in this region, we concluded that the 109-119 Mb region of chromosome 11 harbors a bone size gene that regulates periosteal bone formation. The mutant strain developed in this study provides an important tool to identify a novel mechanosensitive gene that determines bone size during postnatal development.
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Affiliation(s)
- Bouchra Edderkaoui
- Musculoskeletal Disease Center, Loma Linda VA Health Care Systems, Loma Linda, California
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35
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A deep intronic mutation in the ankyrin-1 gene causes diminished protein expression resulting in hemolytic anemia in mice. G3-GENES GENOMES GENETICS 2013; 3:1687-95. [PMID: 23934996 PMCID: PMC3789793 DOI: 10.1534/g3.113.007013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Linkage between transmembrane proteins and the spectrin-based cytoskeleton is necessary for membrane elasticity of red blood cells. Mutations of the proteins that mediate this linkage result in various types of hemolytic anemia. Here we report a novel N-ethyl-N-nitrosourea-induced mutation of ankyrin-1, named hema6, which causes hereditary spherocytosis in mice through a mild reduction of protein expression. The causal mutation was traced to a single nucleotide transition located deep into intron 13 of gene Ank1. In vitro minigene splicing assay revealed two abnormally spliced transcripts containing cryptic exons from fragments of Ank1 intron 13. The inclusion of cryptic exons introduced a premature termination codon, which leads to nonsense-mediated decay of the mutant transcripts in vivo. Hence, in homozygous mice, only wild-type ankyrin-1 is expressed, albeit at 70% of the level in wild-type mice. Heterozygotes display a similar hereditary spherocytosis phenotype stemming from intermediate protein expression level, indicating the haploinsufficiency of the mutation. Weakened linkage between integral transmembrane protein, band 3, and underlying cytoskeleton was observed in mutant mice as the result of reduced high-affinity binding sites provided by ankyrin-1. Hema6 is the only known mouse mutant of Ank1 allelic series that expresses full-length canonical ankyrin-1 at a reduced level, a fact that makes it particularly useful to study the functional impact of ankyrin-1 quantitative deficiency.
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Heterozygous mis-sense mutations in Prkcb as a critical determinant of anti-polysaccharide antibody formation. Genes Immun 2013; 14:223-33. [PMID: 23552399 PMCID: PMC3676473 DOI: 10.1038/gene.2013.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
To identify rate-limiting steps in T cell-independent type 2 (TI-2) antibody production against polysaccharide antigens, we performed a genome-wide screen by immunizing several hundred pedigrees of C57BL/6 mice segregating ENU-induced mis-sense mutations. Two independent mutations, Tilcara and Untied, were isolated that semi-dominantly diminished antibody against polysaccharide but not protein antigens. Both mutations resulted from single amino acid substitutions within the kinase domain of Protein Kinase C Beta (PKCβ). In Tilcara, a Ser552>Pro mutation occurred in helix G, in close proximity to a docking site for the inhibitory N-terminal pseudosubstrate domain of the enzyme, resulting in almost complete loss of active, autophosphorylated PKCβI whereas the amount of alternatively spliced PKCβII protein was not markedly reduced. Circulating B cell subsets were normal and acute responses to BCR-stimulation such as CD25 induction and initiation of DNA synthesis were only measurably diminished in Tilcara homozygotes, whereas the fraction of cells that had divided multiple times was decreased to an intermediate degree in heterozygotes. These results, coupled with evidence of numerous mis-sense PRKCB mutations in the human genome, identify Prkcb as a genetically sensitive step likely to contribute substantially to population variability in anti-polysaccharide antibody levels.
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37
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Brandl K, Beutler B. Creating diseases to understand what prevents them: genetic analysis of inflammation in the gastrointestinal tract. Curr Opin Immunol 2012; 24:678-85. [PMID: 23123276 DOI: 10.1016/j.coi.2012.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 10/10/2012] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases (IBD), including both ulcerative colitis and Crohn's disease, are extremely variable in severity and have strong genetic components. In mice, several mutations are known to favor or inhibit intestinal inflammation. But a comprehensive picture of the pathogenesis of IBD cannot be assembled based on the limited information so far available from mouse genetic analyses, nor can human IBD be stringently ascribed to mutations known to be influential in mice. This review highlights recent progress made using mouse models created through a forward genetic approach towards the understanding of genes that normally prevent intestinal inflammation.
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Affiliation(s)
- Katharina Brandl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, United States
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38
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Abstract
Functional annotation of every gene in the mouse genome is a herculean task that requires a multifaceted approach. Many large-scale initiatives are contributing to this undertaking. The International Knockout Mouse Consortium (IKMC) plans to mutate every protein-coding gene, using a combination of gene trapping and gene targeting in embryonic stem cells. Many other groups are performing using the chemical mutagen ethylnitrosourea (ENU) or transpon-based systems to induce mutations, screening offspring for phenovariants and identifying the causative mutations. A recent paper in BMC Research Notes by Arnold et al. presents data from an ENU-based mutagenesis project that provides not only some of the first phenotype-genotype information for a large number of genes, but also a trove of information, all publicly available, that demonstrates the specificity and efficiency of ENU mutagenesis.
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Affiliation(s)
- Teresa M Gunn
- McLaughlin Research Institute, 1520 23rd St S, Great Falls, MT 59405, USA.
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