51
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Helios is a key transcriptional regulator of outer hair cell maturation. Nature 2018; 563:696-700. [PMID: 30464345 PMCID: PMC6542691 DOI: 10.1038/s41586-018-0728-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/25/2018] [Indexed: 11/09/2022]
Abstract
The sensory cells that are responsible for hearing include the cochlear inner hair cells (IHCs) and outer hair cells (OHCs), with the OHCs being necessary for sound sensitivity and tuning1. Both cell types are thought to arise from common progenitors; however, our understanding of the factors that control the fate of IHCs and OHCs remains limited. Here we identify Ikzf2 (which encodes Helios) as an essential transcription factor in mice that is required for OHC functional maturation and hearing. Helios is expressed in postnatal mouse OHCs, and in the cello mouse model a point mutation in Ikzf2 causes early-onset sensorineural hearing loss. Ikzf2cello/cello OHCs have greatly reduced prestin-dependent electromotile activity, a hallmark of OHC functional maturation, and show reduced levels of crucial OHC-expressed genes such as Slc26a5 (which encodes prestin) and Ocm. Moreover, we show that ectopic expression of Ikzf2 in IHCs: induces the expression of OHC-specific genes; reduces the expression of canonical IHC genes; and confers electromotility to IHCs, demonstrating that Ikzf2 can partially shift the IHC transcriptome towards an OHC-like identity.
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52
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Esapa CT, Piret SE, Nesbit MA, Thomas GP, Coulton LA, Gallagher OM, Simon MM, Kumar S, Mallon AM, Bellantuono I, Brown MA, Croucher PI, Potter PK, Brown SD, Cox RD, Thakker RV. An N-Ethyl- N-Nitrosourea (ENU) Mutagenized Mouse Model for Autosomal Dominant Nonsyndromic Kyphoscoliosis Due to Vertebral Fusion. JBMR Plus 2018; 2:154-163. [PMID: 30283900 PMCID: PMC6124210 DOI: 10.1002/jbm4.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 01/01/2018] [Accepted: 01/14/2018] [Indexed: 02/06/2023] Open
Abstract
Kyphosis and scoliosis are common spinal disorders that occur as part of complex syndromes or as nonsyndromic, idiopathic diseases. Familial and twin studies implicate genetic involvement, although the causative genes for idiopathic kyphoscoliosis remain to be identified. To facilitate these studies, we investigated progeny of mice treated with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and assessed them for morphological and radiographic abnormalities. This identified a mouse with kyphoscoliosis due to fused lumbar vertebrae, which was inherited as an autosomal dominant trait; the phenotype was designated as hereditary vertebral fusion (HVF) and the locus as Hvf. Micro-computed tomography (μCT) analysis confirmed the occurrence of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae in HVF mice, consistent with a pattern of blocked vertebrae due to failure of segmentation. μCT scans also showed the lumbar vertebral column of HVF mice to have generalized disc narrowing, displacement with compression of the neural spine, and distorted transverse processes. Histology of lumbar vertebrae revealed HVF mice to have irregularly shaped vertebral bodies and displacement of intervertebral discs and ossification centers. Genetic mapping using a panel of single nucleotide polymorphic (SNP) loci arranged in chromosome sets and DNA samples from 23 HVF (eight males and 15 females) mice, localized Hvf to chromosome 4A3 and within a 5-megabase (Mb) region containing nine protein coding genes, two processed transcripts, three microRNAs, five small nuclear RNAs, three large intergenic noncoding RNAs, and 24 pseudogenes. However, genome sequence analysis in this interval did not identify any abnormalities in the coding exons, or exon-intron boundaries of any of these genes. Thus, our studies have established a mouse model for a monogenic form of nonsyndromic kyphoscoliosis due to fusion of lumbar vertebrae, and further identification of the underlying genetic defect will help elucidate the molecular mechanisms involved in kyphoscoliosis. © 2018 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
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Affiliation(s)
- Christopher T Esapa
- Academic Endocrine Unit Radcliffe Department of Medicine University of Oxford Oxford Centre for Diabetes, Endocrinology and Metabolism Churchill Hospital Headington UK.,MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Sian E Piret
- Academic Endocrine Unit Radcliffe Department of Medicine University of Oxford Oxford Centre for Diabetes, Endocrinology and Metabolism Churchill Hospital Headington UK
| | - M Andrew Nesbit
- Academic Endocrine Unit Radcliffe Department of Medicine University of Oxford Oxford Centre for Diabetes, Endocrinology and Metabolism Churchill Hospital Headington UK.,School of Biomedical Sciences Ulster University Coleraine UK
| | - Gethin P Thomas
- Institute of Health and Biomedical Innovation Queensland University of Technology Translational Research Institute Princess Alexandra Hospital Brisbane Australia.,Charles Sturt University Boorooma Street Wagga Wagga Australia
| | - Leslie A Coulton
- The Mellanby Centre for Bone Research University of Sheffield Sheffield UK
| | - Orla M Gallagher
- The Mellanby Centre for Bone Research University of Sheffield Sheffield UK
| | - Michelle M Simon
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Saumya Kumar
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK.,Instituto de Medicina Molecular (IMM) Faculdade de Medicina de Universidade de Lisboa Lisboa Portugal
| | - Ann-Marie Mallon
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Ilaria Bellantuono
- The Mellanby Centre for Bone Research University of Sheffield Sheffield UK
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation Queensland University of Technology Translational Research Institute Princess Alexandra Hospital Brisbane Australia
| | - Peter I Croucher
- The Mellanby Centre for Bone Research University of Sheffield Sheffield UK.,Garvan Institute for Medical Research Sydney Australia
| | - Paul K Potter
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Steve Dm Brown
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Roger D Cox
- MRC Mammalian Genetics Unit and Mary Lyon Centre MRC Harwell Institute Harwell Science and Innovation Campus Harwell UK
| | - Rajesh V Thakker
- Academic Endocrine Unit Radcliffe Department of Medicine University of Oxford Oxford Centre for Diabetes, Endocrinology and Metabolism Churchill Hospital Headington UK
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53
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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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54
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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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55
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Li T, Bellen HJ, Groves AK. Using Drosophila to study mechanisms of hereditary hearing loss. Dis Model Mech 2018; 11:11/6/dmm031492. [PMID: 29853544 PMCID: PMC6031363 DOI: 10.1242/dmm.031492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Johnston's organ - the hearing organ of Drosophila - has a very different structure and morphology to that of the hearing organs of vertebrates. Nevertheless, it is becoming clear that vertebrate and invertebrate auditory organs share many physiological, molecular and genetic similarities. Here, we compare the molecular and cellular features of hearing organs in Drosophila with those of vertebrates, and discuss recent evidence concerning the functional conservation of Usher proteins between flies and mammals. Mutations in Usher genes cause Usher syndrome, the leading cause of human deafness and blindness. In Drosophila, some Usher syndrome proteins appear to physically interact in protein complexes that are similar to those described in mammals. This functional conservation highlights a rational role for Drosophila as a model for studying hearing, and for investigating the evolution of auditory organs, with the aim of advancing our understanding of the genes that regulate human hearing and the pathogenic mechanisms that lead to deafness.
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Affiliation(s)
- Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew K Groves
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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56
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Wiwatpanit T, Remis NN, Ahmad A, Zhou Y, Clancy JC, Cheatham MA, García-Añoveros J. Codeficiency of Lysosomal Mucolipins 3 and 1 in Cochlear Hair Cells Diminishes Outer Hair Cell Longevity and Accelerates Age-Related Hearing Loss. J Neurosci 2018; 38:3177-3189. [PMID: 29453205 PMCID: PMC5884457 DOI: 10.1523/jneurosci.3368-17.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/16/2018] [Accepted: 02/02/2018] [Indexed: 01/11/2023] Open
Abstract
Acquired hearing loss is the predominant neurodegenerative condition associated with aging in humans. Although mutations on several genes are known to cause congenital deafness in newborns, few genes have been implicated in age-related hearing loss (ARHL), perhaps because its cause is likely polygenic. Here, we generated mice lacking lysosomal calcium channel mucolipins 3 and 1 and discovered that both male and female mice suffered a polygenic form of hearing loss. Whereas mucolipin 1 is ubiquitously expressed in all cells, mucolipin 3 is expressed in a small subset of cochlear cells, hair cells (HCs) and marginal cells of the stria vascularis, and very few other cell types. Mice lacking both mucolipins 3 and 1, but not either one alone, experienced hearing loss as early as at 1 month of age. The severity of hearing impairment progressed from high to low frequencies and increased with age. Early onset of ARHL in these mice was accompanied by outer HC (OHC) loss. Adult mice conditionally lacking mucolipins in HCs exhibited comparable auditory phenotypes, thereby revealing that the reason for OHC loss is mucolipin codeficiency in the HCs and not in the stria vascularis. Furthermore, we observed that OHCs lacking mucolipins contained abnormally enlarged lysosomes aggregated at the apical region of the cell, whereas other organelles appeared normal. We also demonstrated that these aberrant lysosomes in OHCs lost their membrane integrity through lysosomal membrane permeabilization, a known cause of cellular toxicity that explains why and how OHCs die, leading to premature ARHL.SIGNIFICANCE STATEMENT Presbycusis, or age-related hearing loss (ARHL), is a common characteristic of aging in mammals. Although many genes have been identified to cause deafness from birth in both humans and mice, only a few are known to associate with progressive ARHL, the most prevalent form of deafness. We have found that mice lacking two lysosomal channels, mucolipins 3 and 1, suffer accelerated ARHL due to auditory outer hair cell degeneration, the most common cause of hearing loss and neurodegenerative condition in humans. Lysosomes lacking mucolipins undergo organelle membrane permeabilization and promote cytotoxicity with age, revealing a novel mechanism of outer hair cell degeneration and ARHL. These results underscore the importance of lysosomes in hair cell survival and the maintenance of hearing.
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Affiliation(s)
- Teerawat Wiwatpanit
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, Illinois 60611
- Department of Anesthesiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
| | - Natalie N Remis
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, Illinois 60611
- Department of Anesthesiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
| | - Aisha Ahmad
- Communication Sciences and Disorders Knowles Hearing Center, Northwestern University, Evanston, Illinois 60208
| | - Yingjie Zhou
- Communication Sciences and Disorders Knowles Hearing Center, Northwestern University, Evanston, Illinois 60208
| | - John C Clancy
- Department of Anesthesiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
| | - Mary Ann Cheatham
- Communication Sciences and Disorders Knowles Hearing Center, Northwestern University, Evanston, Illinois 60208
- Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Chicago, Illinois 60611, and
| | - Jaime García-Añoveros
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, Illinois 60611,
- Department of Anesthesiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
- Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Chicago, Illinois 60611, and
- Departments of Neurology and Physiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
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57
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Parker MD. Mouse models of SLC4-linked disorders of HCO 3--transporter dysfunction. Am J Physiol Cell Physiol 2018; 314:C569-C588. [PMID: 29384695 DOI: 10.1152/ajpcell.00301.2017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The SLC4 family Cl-/[Formula: see text] cotransporters (NBCe1, NBCe2, NBCn1, and NBCn2) contribute to a variety of vital physiological processes including pH regulation and epithelial fluid secretion. Accordingly, their dysfunction can have devastating effects. Disorders such as epilepsy, hemolytic anemia, glaucoma, hearing loss, osteopetrosis, and renal tubular acidosis are all genetically linked to SLC4-family gene loci. This review summarizes how studies of Slc4-modified mice have enhanced our understanding of the etiology of SLC4-linked pathologies and the interpretation of genetic linkage studies. The review also surveys the novel disease signs exhibited by Slc4-modified mice which could either be considered to presage their description in humans, or to highlight interspecific differences. Finally, novel Slc4-modified mouse models are proposed, the study of which may further our understanding of the basis and treatment of SLC4-linked disorders of [Formula: see text]-transporter dysfunction.
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Affiliation(s)
- Mark D Parker
- Department of Physiology and Biophysics, The State University of New York: The University at Buffalo , Buffalo, New York.,Department of Ophthalmology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo: The State University of New York , Buffalo, New York.,State University of New York Eye Institutes, University at Buffalo: The State University of New York , Buffalo, New York
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58
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Bowl MR, Simon MM, Ingham NJ, Greenaway S, Santos L, Cater H, Taylor S, Mason J, Kurbatova N, Pearson S, Bower LR, Clary DA, Meziane H, Reilly P, Minowa O, Kelsey L, Tocchini-Valentini GP, Gao X, Bradley A, Skarnes WC, Moore M, Beaudet AL, Justice MJ, Seavitt J, Dickinson ME, Wurst W, de Angelis MH, Herault Y, Wakana S, Nutter LMJ, Flenniken AM, McKerlie C, Murray SA, Svenson KL, Braun RE, West DB, Lloyd KCK, Adams DJ, White J, Karp N, Flicek P, Smedley D, Meehan TF, Parkinson HE, Teboul LM, Wells S, Steel KP, Mallon AM, Brown SDM. A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction. Nat Commun 2017; 8:886. [PMID: 29026089 PMCID: PMC5638796 DOI: 10.1038/s41467-017-00595-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 07/12/2017] [Indexed: 01/27/2023] Open
Abstract
The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function.The full extent of the genetic basis for hearing impairment is unknown. Here, as part of the International Mouse Phenotyping Consortium, the authors perform a hearing loss screen in 3006 mouse knockout strains and identify 52 new candidate genes for genetic hearing loss.
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Affiliation(s)
- Michael R Bowl
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle M Simon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Neil J Ingham
- King's College London, London, SE1 1UL, UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Simon Greenaway
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Luis Santos
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sarah Taylor
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Jeremy Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Natalja Kurbatova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Selina Pearson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Lynette R Bower
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - Dave A Clary
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - Hamid Meziane
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
| | - Patrick Reilly
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
| | - Osamu Minowa
- RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Lois Kelsey
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Glauco P Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, I-00015, Monterotondo Scalo, Italy
| | - Xiang Gao
- SKL of Pharmaceutical Biotechnology and Model Animal Research Center, Collaborative Innovation Center for Genetics and Development, Nanjing Biomedical Research Institute, Nanjing University, 210061, Nanjing, China
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - William C Skarnes
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark Moore
- IMPC, San Anselmo, California, 94960, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Monica J Justice
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - John Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany
| | - Yann Herault
- CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, Illkirch-Graffenstaden, F-67404, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 67404, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France
| | | | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Ann M Flenniken
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | - Colin McKerlie
- The Centre for Phenogenomics, Toronto, Ontario, Canada, M5T 3H7
- The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
- Canada and Mount Sinai Hospital, Toronto, Ontario, Canada, M5G 1X5
| | | | | | | | - David B West
- Childrens' Hospital Oakland Research Institute, Oakland, California, 94609, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, California, 95618, USA
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jacqui White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Natasha Karp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | | | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Helen E Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1 SD, UK
| | - Lydia M Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Karen P Steel
- King's College London, London, SE1 1UL, UK
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK.
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59
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An siRNA-based screen in C2C12 myoblasts identifies novel genes involved in myogenic differentiation. Exp Cell Res 2017; 359:145-153. [DOI: 10.1016/j.yexcr.2017.07.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/16/2017] [Accepted: 07/31/2017] [Indexed: 11/19/2022]
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60
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Bains RS, Wells S, Sillito RR, Armstrong JD, Cater HL, Banks G, Nolan PM. Assessing mouse behaviour throughout the light/dark cycle using automated in-cage analysis tools. J Neurosci Methods 2017; 300:37-47. [PMID: 28456660 PMCID: PMC5909039 DOI: 10.1016/j.jneumeth.2017.04.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/21/2017] [Accepted: 04/22/2017] [Indexed: 12/15/2022]
Abstract
Automated assessment of mouse home-cage behaviour is robust and reliable. Analysis over multiple light/dark cycles improves ability to classify behaviours. Combined RFID and video analysis enables home-cage analysis in group housed animals.
An important factor in reducing variability in mouse test outcomes has been to develop assays that can be used for continuous automated home cage assessment. Our experience has shown that this has been most evidenced in long-term assessment of wheel-running activity in mice. Historically, wheel-running in mice and other rodents have been used as a robust assay to determine, with precision, the inherent period of circadian rhythms in mice. Furthermore, this assay has been instrumental in dissecting the molecular genetic basis of mammalian circadian rhythms. In teasing out the elements of this test that have determined its robustness – automated assessment of an unforced behaviour in the home cage over long time intervals – we and others have been investigating whether similar test apparatus could be used to accurately discriminate differences in distinct behavioural parameters in mice. Firstly, using these systems, we explored behaviours in a number of mouse inbred strains to determine whether we could extract biologically meaningful differences. Secondly, we tested a number of relevant mutant lines to determine how discriminative these parameters were. Our findings show that, when compared to conventional out-of-cage phenotyping, a far deeper understanding of mouse mutant phenotype can be established by monitoring behaviour in the home cage over one or more light:dark cycles.
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Affiliation(s)
- Rasneer S Bains
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Sara Wells
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | | | - J Douglas Armstrong
- Actual Analytics Ltd., Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Heather L Cater
- Mary Lyon Centre, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Gareth Banks
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK
| | - Patrick M Nolan
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science Campus, Oxfordshire, UK.
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Pierrache LHM, Kimchi A, Ratnapriya R, Roberts L, Astuti GDN, Obolensky A, Beryozkin A, Tjon-Fo-Sang MJH, Schuil J, Klaver CCW, Bongers EMHF, Haer-Wigman L, Schalij N, Breuning MH, Fischer GM, Banin E, Ramesar RS, Swaroop A, van den Born LI, Sharon D, Cremers FPM. Whole-Exome Sequencing Identifies Biallelic IDH3A Variants as a Cause of Retinitis Pigmentosa Accompanied by Pseudocoloboma. Ophthalmology 2017; 124:992-1003. [PMID: 28412069 DOI: 10.1016/j.ophtha.2017.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 12/25/2022] Open
Abstract
PURPOSE To identify the genetic cause of and describe the phenotype in 4 families with autosomal recessive retinitis pigmentosa (arRP) that can be associated with pseudocoloboma. DESIGN Case series. PARTICIPANTS Seven patients from 4 unrelated families with arRP, among whom 3 patients had bilateral early-onset macular pseudocoloboma. METHODS We performed homozygosity mapping and whole-exome sequencing in 5 probands and 2 unaffected family members from 4 unrelated families. Subsequently, Sanger sequencing and segregation analysis were performed in additional family members. We reviewed the medical history of individuals carrying IDH3A variants and performed additional ophthalmic examinations, including full-field electroretinography, fundus photography, fundus autofluorescence imaging, and optical coherence tomography. MAIN OUTCOME MEASURES IDH3A variants, age at diagnosis, visual acuity, fundus appearance, visual field, and full-field electroretinography, fundus autofluorescence, and optical coherence tomography findings. RESULTS We identified 7 different variants in IDH3A in 4 unrelated families, that is, 5 missense, 1 nonsense, and 1 frameshift variant. All participants showed symptoms early in life, ranging from night blindness to decreased visual acuity, and were diagnosed between the ages of 1 and 11 years. Four participants with biallelic IDH3A variants displayed a typical arRP phenotype and 3 participants were diagnosed with arRP and pseudocoloboma of the macula. CONCLUSIONS IDH3A variants were identified as a novel cause of typical arRP in some individuals associated with macular pseudocoloboma. We observed both phenotypes in 2 siblings carrying the same compound heterozygous variants, which could be explained by variable disease expression and warrants caution when making assertions about genotype-phenotype correlations.
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Affiliation(s)
- Laurence H M Pierrache
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands; Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adva Kimchi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Roberts
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands; Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Jose Schuil
- Bartiméus Institute for the Visually Impaired, Zeist, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Schalij
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn H Breuning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gratia M Fischer
- Department of Ophthalmology, Dr. George Mukhari Academic Hospital, Sefako Makgatho Health Sciences University (SMU), Ga-Rankuwa, Pretoria, South Africa
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Raj S Ramesar
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands; Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Yang YM, Wang LY. Ageing brains attend a symphony with asynchronous transmitter release. J Physiol 2017; 595:613-614. [PMID: 28145009 DOI: 10.1113/jp273421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Yi-Mei Yang
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth Campus, 1035 University Drive, Duluth, MN, 55812, USA
| | - Lu-Yang Wang
- Program in Neurosciences and Mental Health, SickKids Research Institute and Department of Physiology, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
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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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