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Papaioannou VE, Behringer RR. Strategies for Maintaining Mouse Mutations. Cold Spring Harb Protoc 2024; 2024:107960. [PMID: 37932086 DOI: 10.1101/pdb.over107960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Rules for naming a new mutation are provided. The majority of new mutations are recessive and thus easily maintained in a mouse strain. Considerations on the choice of genetic background are given, depending on how the mutant was produced and how you intend to analyze it. General information on maintaining a mutant colony to perpetuate the mutation and to efficiently produce homozygous mutant mice for analysis is provided. Also discussed are special breeding techniques to delete a selection cassette in vivo, if you produced the mutation in embryonic stem (ES) cells, and to maintain a mutant with a balancer chromosome. In the event of either male or female infertility in the heterozygotes, assisted reproductive techniques may be necessary.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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2
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Papaioannou VE, Behringer RR. Mouse Gene-Targeting Strategies for Maximum Ease and Versatility. Cold Spring Harb Protoc 2024; 2024:107957. [PMID: 37932102 DOI: 10.1101/pdb.over107957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Well-planned strategies are an essential prerequisite for any mutational analysis involving gene targeting. Consideration of the advantages or disadvantages of different methods will aid in the production of a final product that is both technically feasible and versatile. Strategies for gene-targeting experiments in the mouse are discussed, including the rationale behind some of the common elements of gene-targeting vectors, such as homologous DNA and the use of different site-specific recombinases. We detail positive and negative selection as well as screening strategies for homologous recombination events in embryonic stem (ES) cells. For the planning stages of making different types of alleles, we first consider general strategies and then provide details specific to either homologous recombination in ES cells or making alleles by gene editing with CRISPR-Cas in preimplantation embryos. The types of alleles considered are null or knockout alleles, reporter gene knock-in alleles, point mutations, and conditional null alleles.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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3
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Cheong SS, Luis TC, Stewart M, Hillier R, Hind M, Dean CH. A method for TAT-Cre recombinase-mediated floxed allele modification in ex vivo tissue slices. Dis Model Mech 2023; 16:dmm050267. [PMID: 37828896 PMCID: PMC10629676 DOI: 10.1242/dmm.050267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023] Open
Abstract
Precision-cut lung slices (PCLS) are used for a variety of applications. However, methods to manipulate genes in PCLS are currently limited. We developed a new method, TAT-Cre recombinase-mediated floxed allele modification in tissue slices (TReATS), to induce highly effective and temporally controlled gene deletion or activation in ex vivo PCLS. Treatment of PCLS from Rosa26-flox-stop-flox-EYFP mice with cell-permeant TAT-Cre recombinase induced ubiquitous EYFP protein expression, indicating successful Cre-mediated excision of the upstream loxP-flanked stop sequence. Quantitative real-time PCR confirmed induction of EYFP. We successfully replicated the TReATS method in PCLS from Vangl2flox/flox mice, leading to the deletion of loxP-flanked exon 4 of the Vangl2 gene. Cre-treated Vangl2flox/flox PCLS exhibited cytoskeletal abnormalities, a known phenotype caused by VANGL2 dysfunction. We report a new method that bypasses conventional Cre-Lox breeding, allowing rapid and highly effective gene manipulation in ex vivo tissue models.
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Affiliation(s)
- Sek-Shir Cheong
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
| | - Tiago C. Luis
- Centre for Inflammatory Diseases, Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Michelle Stewart
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Rosie Hillier
- The Mary Lyon Centre at MRC Harwell, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Matthew Hind
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
- National Institute for Health Research (NIHR) Respiratory Biomedical Research Unit at the Royal Brompton and Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Charlotte H. Dean
- National Heart and Lung Institute (NHLI), Imperial College London, London SW7 2AZ, UK
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4
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Barbayianni I, Kanellopoulou P, Fanidis D, Nastos D, Ntouskou ED, Galaris A, Harokopos V, Hatzis P, Tsitoura E, Homer R, Kaminski N, Antoniou KM, Crestani B, Tzouvelekis A, Aidinis V. SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis. Nat Commun 2023; 14:5882. [PMID: 37735172 PMCID: PMC10514346 DOI: 10.1038/s41467-023-41614-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023] Open
Abstract
The activation and accumulation of lung fibroblasts resulting in aberrant deposition of extracellular matrix components, is a pathogenic hallmark of Idiopathic Pulmonary Fibrosis, a lethal and incurable disease. In this report, increased expression of TKS5, a scaffold protein essential for the formation of podosomes, was detected in the lung tissue of Idiopathic Pulmonary Fibrosis patients and bleomycin-treated mice. Τhe profibrotic milieu is found to induce TKS5 expression and the formation of prominent podosome rosettes in lung fibroblasts, that are retained ex vivo, culminating in increased extracellular matrix invasion. Tks5+/- mice are found resistant to bleomycin-induced pulmonary fibrosis, largely attributed to diminished podosome formation in fibroblasts and decreased extracellular matrix invasion. As computationally predicted, inhibition of src kinase is shown to potently attenuate podosome formation in lung fibroblasts and extracellular matrix invasion, and bleomycin-induced pulmonary fibrosis, suggesting pharmacological targeting of podosomes as a very promising therapeutic option in pulmonary fibrosis.
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Affiliation(s)
- Ilianna Barbayianni
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Paraskevi Kanellopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Dionysios Fanidis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Dimitris Nastos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Eleftheria-Dimitra Ntouskou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Apostolos Galaris
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Vaggelis Harokopos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Eliza Tsitoura
- Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Katerina M Antoniou
- Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Bruno Crestani
- Department of Pulmonology, Bichat-Claude Bernard Hospital, Paris, France
| | - Argyrios Tzouvelekis
- Department of Respiratory Medicine, School of Medicine, University of Patras, Patras, Greece
| | - Vassilis Aidinis
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece.
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5
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Ali Khan A, Valera Vazquez G, Gustems M, Matteoni R, Song F, Gormanns P, Fessele S, Raess M, Hrabĕ de Angelis M. INFRAFRONTIER: mouse model resources for modelling human diseases. Mamm Genome 2023:10.1007/s00335-023-10010-7. [PMID: 37468728 PMCID: PMC10382402 DOI: 10.1007/s00335-023-10010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/01/2023] [Indexed: 07/21/2023]
Abstract
Over the last decade, INFRAFRONTIER has positioned itself as a world-class Research Infrastructure for the generation, phenotyping, archiving, and distribution of mouse models in Europe. The INFRAFRONTIER network consists of 22 partners from 15 countries, and is continuously enhancing and broadening its portfolio of resources and services that are offered to the research community on a non-profit basis. By bringing together European rodent model expertise and providing valuable disease model services to the biomedical research community, INFRAFRONTIER strives to push the accessibility of cutting-edge human disease modelling technologies across the European research landscape. This article highlights the latest INFRAFRONTIER developments and informs the research community about its extensively utilised services, resources, and technical developments, specifically the intricacies of the INFRAFRONTIER database, use of Curated Disease Models, overview of the INFRAFRONTIER Cancer and Rare Disease resources, and information about its main state-of-the-art services.
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Affiliation(s)
| | | | | | - Rafaele Matteoni
- Institute of Biochemistry and Cell Biology, Italian National Research Council (CNR), Monterotondo, Rome, Italy
| | - Fei Song
- INFRAFRONTIER GmbH, Neuherberg, Germany
| | | | | | | | - Martin Hrabĕ de Angelis
- INFRAFRONTIER GmbH, Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München (HMGU-IEG), Neuherberg, Germany
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Knockout of the Complex III subunit Uqcrh causes bioenergetic impairment and cardiac contractile dysfunction. Mamm Genome 2022:10.1007/s00335-022-09973-w. [PMID: 36565314 DOI: 10.1007/s00335-022-09973-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/03/2022] [Indexed: 12/25/2022]
Abstract
Ubiquinol cytochrome c reductase hinge protein (UQCRH) is required for the electron transfer between cytochrome c1 and c of the mitochondrial cytochrome bc1 Complex (CIII). A two-exon deletion in the human UQCRH gene has recently been identified as the cause for a rare familial mitochondrial disorder. Deletion of the corresponding gene in the mouse (Uqcrh-KO) resulted in striking biochemical and clinical similarities including impairment of CIII, failure to thrive, elevated blood glucose levels, and early death. Here, we set out to test how global ablation of the murine Uqcrh affects cardiac morphology and contractility, and bioenergetics. Hearts from Uqcrh-KO mutant mice appeared macroscopically considerably smaller compared to wildtype littermate controls despite similar geometries as confirmed by transthoracic echocardiography (TTE). Relating TTE-assessed heart to body mass revealed the development of subtle cardiac enlargement, but histopathological analysis showed no excess collagen deposition. Nonetheless, Uqcrh-KO hearts developed pronounced contractile dysfunction. To assess mitochondrial functions, we used the high-resolution respirometer NextGen-O2k allowing measurement of mitochondrial respiratory capacity through the electron transfer system (ETS) simultaneously with the redox state of ETS-reactive coenzyme Q (Q), or production of reactive oxygen species (ROS). Compared to wildtype littermate controls, we found decreased mitochondrial respiratory capacity and more reduced Q in Uqcrh-KO, indicative for an impaired ETS. Yet, mitochondrial ROS production was not generally increased. Taken together, our data suggest that Uqcrh-KO leads to cardiac contractile dysfunction at 9 weeks of age, which is associated with impaired bioenergetics but not with mitochondrial ROS production. Global ablation of the Uqcrh gene results in functional impairment of CIII associated with metabolic dysfunction and postnatal developmental arrest immediately after weaning from the mother. Uqcrh-KO mice show dramatically elevated blood glucose levels and decreased ability of isolated cardiac mitochondria to consume oxygen (O2). Impaired development (failure to thrive) after weaning manifests as a deficiency in the gain of body mass and growth of internal organ including the heart. The relative heart mass seemingly increases when organ mass calculated from transthoracic echocardiography (TTE) is normalized to body mass. Notably, the heart shows no signs of collagen deposition, yet does develop a contractile dysfunction reflected by a decrease in ejection fraction and fractional shortening.
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Oh RY, Deshwar AR, Marwaha A, Sabha N, Tropak M, Hou H, Yuki KE, Wilson MD, Rump P, Lunsing R, Elserafy N, Chung CWT, Hewson S, Klein-Rodewald T, Calzada-Wack J, Sanz-Moreno A, Kraiger M, Marschall S, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Dowling J, Schulze A. Biallelic loss-of-function variants in RABGAP1 cause a novel neurodevelopmental syndrome. Genet Med 2022; 24:2399-2407. [PMID: 36083289 DOI: 10.1016/j.gim.2022.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
PURPOSE RABGAP1 is a GTPase-activating protein implicated in a variety of cellular and molecular processes, including mitosis, cell migration, vesicular trafficking, and mTOR signaling. There are no known Mendelian diseases caused by variants in RABGAP1. METHODS Through GeneMatcher, we identified 5 patients from 3 unrelated families with homozygous variants in the RABGAP1 gene found on exome sequencing. We established lymphoblastoid cells lines derived from an affected individual and her parents and performed RNA sequencing and functional studies. Rabgap1 knockout mice were generated and phenotyped. RESULTS We report 5 patients presenting with a common constellation of features, including global developmental delay/intellectual disability, microcephaly, bilateral sensorineural hearing loss, and seizures, as well as overlapping dysmorphic features. Neuroimaging revealed common features, including delayed myelination, white matter volume loss, ventriculomegaly, and thinning of the corpus callosum. Functional analysis of patient cells revealed downregulated mTOR signaling and abnormal localization of early endosomes and lysosomes. Rabgap1 knockout mice exhibited several features in common with the patient cohort, including microcephaly, thinning of the corpus callosum, and ventriculomegaly. CONCLUSION Collectively, our results provide evidence of a novel neurodevelopmental syndrome caused by biallelic loss-of-function variants in RABGAP1.
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Affiliation(s)
- Rachel Youjin Oh
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ashish R Deshwar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ashish Marwaha
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - Nesrin Sabha
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Tropak
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Huayun Hou
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyoko E Yuki
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Roelineke Lunsing
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Noha Elserafy
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Clara W T Chung
- Department of Clinical Genetics, Liverpool Hospital, Sydney, New South Wales, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Stacy Hewson
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Adrián Sanz-Moreno
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Markus Kraiger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Susan Marschall
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße, 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, Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstraße, Neuherberg, Germany
| | - James Dowling
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Neurology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andreas Schulze
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada; Departments of Paediatrics and Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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Mutations in MINAR2 encoding membrane integral NOTCH2-associated receptor 2 cause deafness in humans and mice. Proc Natl Acad Sci U S A 2022; 119:e2204084119. [PMID: 35727972 PMCID: PMC9245706 DOI: 10.1073/pnas.2204084119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Discovery of deafness genes and elucidating their functions have substantially contributed to our understanding of hearing physiology and its pathologies. Here we report on DNA variants in MINAR2, encoding membrane integral NOTCH2-associated receptor 2, in four families underlying autosomal recessive nonsyndromic deafness. Neurologic evaluation of affected individuals at ages ranging from 4 to 80 y old does not show additional abnormalities. MINAR2 is a recently annotated gene with limited functional understanding. We detected three MINAR2 variants, c.144G > A (p.Trp48*), c.412_419delCGGTTTTG (p.Arg138Valfs*10), and c.393G > T, in 13 individuals with congenital- or prelingual-onset severe-to-profound sensorineural hearing loss (HL). The c.393G > T variant is shown to disrupt a splice donor site. We show that Minar2 is expressed in the mouse inner ear, with the protein localizing mainly in the hair cells, spiral ganglia, the spiral limbus, and the stria vascularis. Mice with loss of function of the Minar2 protein (Minar2tm1b/tm1b) present with rapidly progressive sensorineural HL associated with a reduction in outer hair cell stereocilia in the shortest row and degeneration of hair cells at a later age. We conclude that MINAR2 is essential for hearing in humans and mice and its disruption leads to sensorineural HL. Progressive HL observed in mice and in some affected individuals and as well as relative preservation of hair cells provides an opportunity to interfere with HL using genetic therapies.
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Vidali S, Gerlini R, Thompson K, Urquhart JE, Meisterknecht J, Aguilar‐Pimentel JA, Amarie OV, Becker L, Breen C, Calzada‐Wack J, Chhabra NF, Cho Y, da Silva‐Buttkus P, Feichtinger RG, Gampe K, Garrett L, Hoefig KP, Hölter SM, Jameson E, Klein‐Rodewald T, Leuchtenberger S, Marschall S, Mayer‐Kuckuk P, Miller G, Oestereicher MA, Pfannes K, Rathkolb B, Rozman J, Sanders C, Spielmann N, Stoeger C, Szibor M, Treise I, Walter JH, Wurst W, Mayr JA, Fuchs H, Gärtner U, Wittig I, Taylor RW, Newman WG, Prokisch H, Gailus‐Durner V, Hrabě de Angelis M. Characterising a homozygous two-exon deletion in UQCRH: comparing human and mouse phenotypes. EMBO Mol Med 2021; 13:e14397. [PMID: 34750991 PMCID: PMC8649870 DOI: 10.15252/emmm.202114397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial disorders are clinically and genetically diverse, with isolated complex III (CIII) deficiency being relatively rare. Here, we describe two affected cousins, presenting with recurrent episodes of severe lactic acidosis, hyperammonaemia, hypoglycaemia and encephalopathy. Genetic investigations in both cases identified a homozygous deletion of exons 2 and 3 of UQCRH, which encodes a structural complex III (CIII) subunit. We generated a mouse model with the equivalent homozygous Uqcrh deletion (Uqcrh-/- ), which also presented with lactic acidosis and hyperammonaemia, but had a more severe, non-episodic phenotype, resulting in failure to thrive and early death. The biochemical phenotypes observed in patient and Uqcrh-/- mouse tissues were remarkably similar, displaying impaired CIII activity, decreased molecular weight of fully assembled holoenzyme and an increase of an unexpected large supercomplex (SXL ), comprising mostly of one complex I (CI) dimer and one CIII dimer. This phenotypic similarity along with lentiviral rescue experiments in patient fibroblasts verifies the pathogenicity of the shared genetic defect, demonstrating that the Uqcrh-/- mouse is a valuable model for future studies of human CIII deficiency.
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10
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Perry MN, Smith CM, Onda H, Ringwald M, Murray SA, Smith CL. Annotated expression and activity data for murine recombinase alleles and transgenes: the CrePortal resource. Mamm Genome 2021; 33:55-65. [PMID: 34482425 PMCID: PMC8913597 DOI: 10.1007/s00335-021-09909-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/29/2021] [Indexed: 11/30/2022]
Abstract
Recombinase alleles and transgenes can be used to facilitate spatio-temporal specificity of gene disruption or transgene expression. However, the versatility of this in vivo recombination system relies on having detailed and accurate characterization of recombinase expression and activity to enable selection of the appropriate allele or transgene. The CrePortal (http://www.informatics.jax.org/home/recombinase) leverages the informatics infrastructure of Mouse Genome Informatics to integrate data from the scientific literature, direct data submissions from the scientific community at-large, and from major projects developing new recombinase lines and characterizing recombinase expression and specificity patterns. Searching the CrePortal by recombinase activity or specific recombinase gene driver provides users with a recombinase alleles and transgenes activity tissue summary and matrix comparison of gene expression and recombinase activity with links to generation details, a recombinase activity grid, and associated phenotype annotations. Future improvements will add cell type-based activity annotations. The CrePortal provides a comprehensive presentation of recombinase allele and transgene data to assist researchers in selection of the recombinase allele or transgene based on where and when recombination is desired.
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Affiliation(s)
| | | | - Hiroaki Onda
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
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11
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Vashi N, Ackerley C, Post M, Justice MJ. Aberrant lung lipids cause respiratory impairment in a Mecp2-deficient mouse model of Rett syndrome. Hum Mol Genet 2021; 30:2161-2176. [PMID: 34230964 PMCID: PMC8561422 DOI: 10.1093/hmg/ddab182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/11/2021] [Accepted: 06/28/2021] [Indexed: 11/14/2022] Open
Abstract
Severe respiratory impairment is a prominent feature of Rett syndrome (RTT), an X-linked disorder caused by mutations in methyl CpG-binding protein 2 (MECP2). Despite MECP2's ubiquitous expression, respiratory anomalies are attributed to neuronal dysfunction. Here, we show that neutral lipids accumulate in mouse Mecp2-mutant lungs, while surfactant phospholipids decrease. Conditional deletion of Mecp2 from lipid-producing alveolar epithelial 2 (AE2) cells causes aberrant lung lipids and respiratory symptoms, while deletion of Mecp2 from hindbrain neurons results in distinct respiratory abnormalities. Single-cell RNA sequencing of AE2 cells suggests lipid production and storage increase at the expense of phospholipid synthesis. Lipid production enzymes are confirmed as direct targets of MECP2-directed nuclear receptor corepressor 1/2 (NCOR1/2) transcriptional repression. Remarkably, lipid-lowering fluvastatin improves respiratory anomalies in Mecp2-mutant mice. These data implicate autonomous pulmonary loss of MECP2 in respiratory symptoms for the first time and have immediate impacts on patient care.
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Affiliation(s)
- Neeti Vashi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.,Genetics and Genome Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Cameron Ackerley
- Translational Medicine Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Martin Post
- Translational Medicine Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, M5G 0A4, Canada
| | - Monica J Justice
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.,Genetics and Genome Biology Program, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, ON, M5G 0A4, Canada
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12
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Keerthivasan S, Şenbabaoğlu Y, Martinez-Martin N, Husain B, Verschueren E, Wong A, Yang YA, Sun Y, Pham V, Hinkle T, Oei Y, Madireddi S, Corpuz R, Tam L, Carlisle S, Roose-Girma M, Modrusan Z, Ye Z, Koerber JT, Turley SJ. Homeostatic functions of monocytes and interstitial lung macrophages are regulated via collagen domain-binding receptor LAIR1. Immunity 2021; 54:1511-1526.e8. [PMID: 34260887 DOI: 10.1016/j.immuni.2021.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 02/21/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022]
Abstract
Myeloid cells encounter stromal cells and their matrix determinants on a continual basis during their residence in any given organ. Here, we examined the impact of the collagen receptor LAIR1 on myeloid cell homeostasis and function. LAIR1 was highly expressed in the myeloid lineage and enriched in non-classical monocytes. Proteomic definition of the LAIR1 interactome identified stromal factor Colec12 as a high-affinity LAIR1 ligand. Proteomic profiling of LAIR1 signaling triggered by Collagen1 and Colec12 highlighted pathways associated with survival, proliferation, and differentiation. Lair1-/- mice had reduced frequencies of Ly6C- monocytes, which were associated with altered proliferation and apoptosis of non-classical monocytes from bone marrow and altered heterogeneity of interstitial macrophages in lung. Myeloid-specific LAIR1 deficiency promoted metastatic growth in a melanoma model and LAIR1 expression associated with improved clinical outcomes in human metastatic melanoma. Thus, monocytes and macrophages rely on LAIR1 sensing of stromal determinants for fitness and function, with relevance in homeostasis and disease.
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Affiliation(s)
| | | | | | | | | | - Anne Wong
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | - Yoko Oei
- Genentech Inc., South San Francisco, CA, USA
| | | | | | - Lucinda Tam
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | - Zhengmao Ye
- Genentech Inc., South San Francisco, CA, USA
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13
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Bell RMB, Villalobos E, Nixon M, Miguelez-Crespo A, Murphy L, Fawkes A, Coutts A, Sharp MGF, Koerner MV, Allan E, Meijer OC, Houtman R, Odermatt A, Beck KR, Denham SG, Lee P, Homer NZM, Walker BR, Morgan RA. Carbonyl reductase 1 amplifies glucocorticoid action in adipose tissue and impairs glucose tolerance in lean mice. Mol Metab 2021; 48:101225. [PMID: 33785425 PMCID: PMC8095185 DOI: 10.1016/j.molmet.2021.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Carbonyl reductase 1 (Cbr1), a recently discovered contributor to tissue glucocorticoid metabolism converting corticosterone to 20β-dihydrocorticosterone (20β-DHB), is upregulated in adipose tissue of obese humans and mice and may contribute to cardiometabolic complications of obesity. This study tested the hypothesis that Cbr1-mediated glucocorticoid metabolism influences glucocorticoid and mineralocorticoid receptor activation in adipose tissue and impacts glucose homeostasis in lean and obese states. METHODS The actions of 20β-DHB on corticosteroid receptors in adipose tissue were investigated first using a combination of in silico, in vitro, and transcriptomic techniques and then in vivo administration in combination with receptor antagonists. Mice lacking one Cbr1 allele and mice overexpressing Cbr1 in their adipose tissue underwent metabolic phenotyping before and after induction of obesity with high-fat feeding. RESULTS 20β-DHB activated both the glucocorticoid and mineralocorticoid receptor in adipose tissue and systemic administration to wild-type mice induced glucose intolerance, an effect that was ameliorated by both glucocorticoid and mineralocorticoid receptor antagonism. Cbr1 haploinsufficient lean male mice had lower fasting glucose and improved glucose tolerance compared with littermate controls, a difference that was abolished by administration of 20β-DHB and absent in female mice with higher baseline adipose 20β-DHB concentrations than male mice. Conversely, overexpression of Cbr1 in adipose tissue resulted in worsened glucose tolerance and higher fasting glucose in lean male and female mice. However, neither Cbr1 haploinsfficiency nor adipose overexpression affected glucose dyshomeostasis induced by high-fat feeding. CONCLUSIONS Carbonyl reductase 1 is a novel regulator of glucocorticoid and mineralocorticoid receptor activation in adipose tissue that influences glucose homeostasis in lean mice.
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Affiliation(s)
- Rachel M B Bell
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Elisa Villalobos
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Mark Nixon
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Allende Miguelez-Crespo
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Lee Murphy
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Angie Fawkes
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Audrey Coutts
- Genetics Core, Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom.
| | - Matthew G F Sharp
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Martha V Koerner
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Emma Allan
- Transgenics Core, Bioresearch & Veterinary Services, University of Edinburgh, Edinburgh, United Kingdom.
| | - Onno C Meijer
- Department of Internal Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Renè Houtman
- Pamgene International, Den Bosch, the Netherlands.
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Katharina R Beck
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland.
| | - Scott G Denham
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Patricia Lee
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Natalie Z M Homer
- Mass Spectrometry Core Laboratory, Wellcome Trust Clinical Research Facility, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
| | - Brian R Walker
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Ruth A Morgan
- British Heart Foundation Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom; Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom.
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14
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Park SG, Kim EK, Nam KH, Lee JG, Baek IJ, Lee BJ, Nam SY. Heart defects and embryonic lethality in Asb2 knock out mice correlate with placental defects. Cells Dev 2021; 165:203663. [PMID: 33993984 DOI: 10.1016/j.cdev.2021.203663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/03/2021] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Asb2, ankyrin repeat, and SOCS box protein 2 form an E3 ubiquitin ligase complex. Asb2 ubiquitin ligase activity drives the degradation of filamins, which have essential functions in humans. The placenta is a temporary organ that forms during pregnancy, and normal placentation is important for survival and growth of the fetus. Recent studies have shown that approximately 25-30% of knockout (KO) mice have non-viable offspring, and 68% of knockout lines exhibit placental dysmorphologies. There are very few studies on Asb2, with insufficient research on its role in placental development. Therefore, we generated Asb2 knockout mice and undertook to investigate Asb2 expression during organogenesis, and to identify its role in early embryonic and placental development. The external morphology of KO embryos revealed abnormal phenotypes including growth retardation, pericardial effusion, pale color, and especially heart beat defect from E 9.5. Furthermore, Asb2 expression was observed in the heart from E 9.5, indicating that it is specifically expressed during early heart formation, resulting in embryonic lethality. Histological analysis of E 10.5 KO heart showed malformations such as failure of chamber formation, reduction in trabeculated myocardium length, absence of mesenchymal cells, and destruction of myocardium wall. Moreover, the histological results of Asb2-deficient placenta showed abnormal phenotypes including small labyrinth and reduced vascular complexity, indicating that failure to establish mature circulatory pattern affects the embryonic development and results in early mortality. Collectively, our results demonstrate that Asb2 knockout mice have placental defects, that subsequently result in failure to form a normal cardiac septum, and thereby result in embryo mortality in utero at around E 9.5.
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Affiliation(s)
- Seul Gi Park
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Eun-Kyoung Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 34141, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 34141, Republic of Korea
| | - Jong Geol Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - In-Jeoung Baek
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom Jun Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sang-Yoon Nam
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea.
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15
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Thorsen AS, Khamis D, Kemp R, Colombé M, Lourenço FC, Morrissey E, Winton D. Heterogeneity in clone dynamics within and adjacent to intestinal tumours identified by Dre-mediated lineage tracing. Dis Model Mech 2021; 14:dmm046706. [PMID: 33093165 PMCID: PMC7823168 DOI: 10.1242/dmm.046706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/12/2020] [Indexed: 11/20/2022] Open
Abstract
Somatic models of tissue pathology commonly use induction of gene-specific mutations in mice mediated by spatiotemporal regulation of Cre recombinase. Subsequent investigation of the onset and development of disease can be limited by the inability to track changing cellular behaviours over time. Here, a lineage-tracing approach based on ligand-dependent activation of Dre recombinase that can be employed independently of Cre is described. The clonal biology of the intestinal epithelium following Cre-mediated stabilisation of β-catenin reveals that, within tumours, many new clones rapidly become extinct. Surviving clones show accelerated population of tumour glands compared to normal intestinal crypts but in a non-uniform manner, indicating that intra-tumour glands follow heterogeneous dynamics. In tumour-adjacent epithelia, clone sizes are smaller than in the background epithelia, as a whole. This suggests a zone of ∼seven crypt diameters within which clone expansion is inhibited by tumours and that may facilitate their growth.
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Affiliation(s)
- Ann-Sofie Thorsen
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Doran Khamis
- University of Oxford, Center for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Richard Kemp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mathilde Colombé
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Filipe C. Lourenço
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Edward Morrissey
- University of Oxford, Center for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Douglas Winton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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16
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Senger K, Yuan W, Sagolla M, Doerr J, Bolon B, Ziai J, Sun K, Warming S, Roose‐Girma M, Zhang N, Tam L, Newman RJ, Chaudhuri S, Antony A, Goldstein LD, Durinck S, Jaiswal BS, Lafkas D, Modrusan Z, Seshagiri S. Embryonic lethality and defective mammary gland development of activator-function impaired conditional knock-in Erbb3 V943R mice. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 2:e10036. [PMID: 36618440 PMCID: PMC9744554 DOI: 10.1002/ggn2.10036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 01/11/2023]
Abstract
ERBB3 is a pseudokinase domain-containing member of the ERBB family of receptor tyrosine kinases (RTKs). Following ligand binding, ERBB receptors homo- or hetero-dimerize, leading to a head-to-tail arrangement of the intracellular kinase domains, where the "receiver" kinase domain of one ERBB is activated by the "activator" domain of the other ERBB in the dimer. In ERBB3, a conserved valine at codon 943 (V943) in the kinase C-terminal domain has been shown to be important for its function as an "activator" kinase in vitro. Here we report a knock-in mouse model where we have modified the endogenous Erbb3 allele to allow for tissue-specific conditional expression of Erbb3 V943R (Erbb3 CKI-V943R ). Additionally, we generated an Erbb3 D850N (Erbb3 CKI-D850N ) conditional knock-in mouse model where the conserved aspartate in the DFG motif of the pseudokinase domain was mutated to abolish any potential residual kinase activity. While Erbb3 D850N/D850N animals developed normally, homozygous Erbb3 V943R/V943R expression during development resulted in embryonic lethality. Further, tissue specific expression of Erbb3 V943R/V943R in the mammary gland epithelium following its activation using MMTV-Cre resulted in delayed elongation of the ductal network during puberty. Single-cell RNA-seq analysis of Erbb3 V943R/V943R mammary glands showed a reduction in a specific subset of fibrinogen-producing luminal epithelial cells.
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Affiliation(s)
- Kate Senger
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Wenlin Yuan
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Meredith Sagolla
- Department of PathologyGenentechSouth San FranciscoCaliforniaUSA
| | - Jonas Doerr
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | | | - James Ziai
- Department of PathologyGenentechSouth San FranciscoCaliforniaUSA
| | - Kai‐Hui Sun
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Soren Warming
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Merone Roose‐Girma
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Na Zhang
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Lucinda Tam
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Robert J. Newman
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Subhra Chaudhuri
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | | | - Leonard D. Goldstein
- Department of Bioinformatics and Computational BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Steffen Durinck
- Department of Bioinformatics and Computational BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Bijay S. Jaiswal
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Daniel Lafkas
- Department of Immunology DiscoveryGenentechSouth San FranciscoCaliforniaUSA
| | - Zora Modrusan
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA
| | - Somasekar Seshagiri
- Department of Molecular BiologyGenentechSouth San FranciscoCaliforniaUSA,SciGenom Research FoundationBangaloreKarnatakaIndia
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17
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Xie C, Bekpen C, Künzel S, Keshavarz M, Krebs-Wheaton R, Skrabar N, Ullrich KK, Zhang W, Tautz D. Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines. PLoS Comput Biol 2020; 16:e1008354. [PMID: 33180766 PMCID: PMC7685438 DOI: 10.1371/journal.pcbi.1008354] [Citation(s) in RCA: 4] [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: 01/20/2020] [Revised: 11/24/2020] [Accepted: 09/20/2020] [Indexed: 12/26/2022] Open
Abstract
Systematic knockout studies in mice have shown that a large fraction of the gene replacements show no lethal or other overt phenotypes. This has led to the development of more refined analysis schemes, including physiological, behavioral, developmental and cytological tests. However, transcriptomic analyses have not yet been systematically evaluated for non-lethal knockouts. We conducted a power analysis to determine the experimental conditions under which even small changes in transcript levels can be reliably traced. We have applied this to two gene disruption lines of genes for which no function was known so far. Dedicated phenotyping tests informed by the tissues and stages of highest expression of the two genes show small effects on the tested phenotypes. For the transcriptome analysis of these stages and tissues, we used a prior power analysis to determine the number of biological replicates and the sequencing depth. We find that under these conditions, the knockouts have a significant impact on the transcriptional networks, with thousands of genes showing small transcriptional changes. GO analysis suggests that A930004D18Rik is involved in developmental processes through contributing to protein complexes, and A830005F24Rik in extracellular matrix functions. Subsampling analysis of the data reveals that the increase in the number of biological replicates was more important that increasing the sequencing depth to arrive at these results. Hence, our proof-of-principle experiment suggests that transcriptomic analysis is indeed an option to study gene functions of genes with weak or no traceable phenotypic effects and it provides the boundary conditions under which this is possible. Knockout mice benefit the understanding of gene functions in mammals. However, it has proven difficult for many genes to identify clear phenotypes, related due to lack of sufficient assays. As Lewis Wolpert put it in a famous quote “But did you take them to the opera?”, thus metaphorically alluding to the need to extend phenotyping efforts. This insight led to the establishment of phenotyping pipelines that are nowadays routinely used to characterize knock-out lines. However, transcriptomic approaches based on RNA-Seq have been much less explored for such deep-level studies. We conducted here both, a theoretical power analysis and practical RNA-Seq experiments on two knockout lines with small phenotypic effects to investigate the parameters including sample size, sequencing depth, fold change, and dispersion. Our dedicated RNA-Seq studies discovered thousands of genes with small transcriptional changes and enriched in specific functions in both knockout lines. We find that it is more important to increase the number of samples than to increase the sequencing depth. Our work shows that a deep RNA-Seq study on knockouts is powerful for understanding gene functions in cases of weak phenotypic effects, and provides a guideline for the experimental design of such studies.
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Affiliation(s)
- Chen Xie
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Cemalettin Bekpen
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Maryam Keshavarz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Rebecca Krebs-Wheaton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Neva Skrabar
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kristian K. Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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18
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Choi JH, Burke JM, Szymanik KH, Nepal U, Battenhouse A, Lau JT, Stark A, Lam V, Sullivan CS. DUSP11-mediated control of 5'-triphosphate RNA regulates RIG-I sensitivity. Genes Dev 2020; 34:1697-1712. [PMID: 33184222 PMCID: PMC7706711 DOI: 10.1101/gad.340604.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/28/2020] [Indexed: 12/11/2022]
Abstract
In this study, Choi et al. set out to elucidate the physiological role of RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) in the innate immune response. Using in vivo and in vitro experiments, the authors describe the importance of controlling 5′-triphosphate RNA levels to prevent aberrant RIG-I signaling and demonstrate DUSP11 as a key effector of this mechanism. Deciphering the mechanisms that regulate the sensitivity of pathogen recognition receptors is imperative to understanding infection and inflammation. Here we demonstrate that the RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) acts on both host and virus-derived 5′-triphosphate RNAs rendering them less active in inducing a RIG-I-mediated immune response. Reducing DUSP11 levels alters host triphosphate RNA packaged in extracellular vesicles and induces enhanced RIG-I activation in cells exposed to extracellular vesicles. Virus infection of cells lacking DUSP11 results in a higher proportion of triphosphorylated viral transcripts and attenuated virus replication, which is rescued by reducing RIG-I expression. Consistent with the activity of DUSP11 in the cellular RIG-I response, mice lacking DUSP11 display lower viral loads, greater sensitivity to triphosphorylated RNA, and a signature of enhanced interferon activity in select tissues. Our results reveal the importance of controlling 5′-triphosphate RNA levels to prevent aberrant RIG-I signaling and demonstrate DUSP11 as a key effector of this mechanism.
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Affiliation(s)
- Joon H Choi
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - James M Burke
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Kayla H Szymanik
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Upasana Nepal
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Justin T Lau
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Aaron Stark
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Victor Lam
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
| | - Christopher S Sullivan
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin Texas 78712, USA
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19
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Gleeson D, Sethi D, Platte R, Burvill J, Barrett D, Akhtar S, Bruntraeger M, Bottomley J, Mouse Genetics Project S, Bussell J, Ryder E. High-throughput genotyping of high-homology mutant mouse strains by next-generation sequencing. Methods 2020; 191:78-86. [PMID: 33096238 PMCID: PMC8205115 DOI: 10.1016/j.ymeth.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/25/2020] [Accepted: 10/18/2020] [Indexed: 11/05/2022] Open
Abstract
Next generation sequencing is a scalable solution to genotyping mutant mice. Ratios of wild type and mutant sequence counts are used to call the genotype. Hundreds of samples can be multiplexed into one sequencing experiment. Amplification of high-homology genes can be easily filtered out during analysis.
Genotyping of knockout alleles in mice is commonly performed by end-point PCR or gene-specific/universal cassette qPCR. Both have advantages and limitations in terms of assay design and interpretation of results. As an alternative method for high-throughput genotyping, we investigated next generation sequencing (NGS) of PCR amplicons, with a focus on CRISPR-mediated exon deletions where antibiotic selection markers are not present. By multiplexing the wild type and mutant-specific PCR reactions, the genotype can be called by the relative sequence counts of each product. The system is highly scalable and can be applied to a variety of different allele types, including those produced by the International Mouse Phenotyping Consortium and associated projects. One potential challenge with any assay design is locating unique areas of the genome, especially when working with gene families or regions of high homology. These can result in misleading or ambiguous genotypes for either qPCR or end-point assays. Here, we show that genotyping by NGS can negate these issues by simple, automated filtering of undesired sequences. Analysis and genotype calls can also be fully automated, using FASTQ or FASTA input files and an in-house Perl script and SQL database.
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Affiliation(s)
- Diane Gleeson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Debarati Sethi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Radka Platte
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jonathan Burvill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Shaheen Akhtar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Michaela Bruntraeger
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Joanna Bottomley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - James Bussell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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20
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Integration of innate immune signalling by caspase-8 cleavage of N4BP1. Nature 2020; 587:275-280. [PMID: 32971525 DOI: 10.1038/s41586-020-2796-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023]
Abstract
Mutations in the death receptor FAS1,2 or its ligand FASL3 cause autoimmune lymphoproliferative syndrome, whereas mutations in caspase-8 or its adaptor FADD-which mediate cell death downstream of FAS and FASL-cause severe immunodeficiency in addition to autoimmune lymphoproliferative syndrome4-6. Mouse models have corroborated a role for FADD-caspase-8 in promoting inflammatory responses7-12, but the mechanisms that underlie immunodeficiency remain undefined. Here we identify NEDD4-binding protein 1 (N4BP1) as a suppressor of cytokine production that is cleaved and inactivated by caspase-8. N4BP1 deletion in mice increased the production of select cytokines upon stimulation of the Toll-like receptor (TLR)1-TLR2 heterodimer (referred to herein as TLR1/2), TLR7 or TLR9, but not upon engagement of TLR3 or TLR4. N4BP1 did not suppress TLR3 or TLR4 responses in wild-type macrophages, owing to TRIF- and caspase-8-dependent cleavage of N4BP1. Notably, the impaired production of cytokines in response to TLR3 and TLR4 stimulation of caspase-8-deficient macrophages13 was largely rescued by co-deletion of N4BP1. Thus, the persistence of intact N4BP1 in caspase-8-deficient macrophages impairs their ability to mount robust cytokine responses. Tumour necrosis factor (TNF), like TLR3 or TLR4 agonists, also induced caspase-8-dependent cleavage of N4BP1, thereby licensing TRIF-independent TLRs to produce higher levels of inflammatory cytokines. Collectively, our results identify N4BP1 as a potent suppressor of cytokine responses; reveal N4BP1 cleavage by caspase-8 as a point of signal integration during inflammation; and offer an explanation for immunodeficiency caused by mutations of FADD and caspase-8.
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21
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Ndoja A, Reja R, Lee SH, Webster JD, Ngu H, Rose CM, Kirkpatrick DS, Modrusan Z, Chen YJJ, Dugger DL, Gandham V, Xie L, Newton K, Dixit VM. Ubiquitin Ligase COP1 Suppresses Neuroinflammation by Degrading c/EBPβ in Microglia. Cell 2020; 182:1156-1169.e12. [PMID: 32795415 DOI: 10.1016/j.cell.2020.07.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/09/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Dysregulated microglia are intimately involved in neurodegeneration, including Alzheimer's disease (AD) pathogenesis, but the mechanisms controlling pathogenic microglial gene expression remain poorly understood. The transcription factor CCAAT/enhancer binding protein beta (c/EBPβ) regulates pro-inflammatory genes in microglia and is upregulated in AD. We show expression of c/EBPβ in microglia is regulated post-translationally by the ubiquitin ligase COP1 (also called RFWD2). In the absence of COP1, c/EBPβ accumulates rapidly and drives a potent pro-inflammatory and neurodegeneration-related gene program, evidenced by increased neurotoxicity in microglia-neuronal co-cultures. Antibody blocking studies reveal that neurotoxicity is almost entirely attributable to complement. Remarkably, loss of a single allele of Cebpb prevented the pro-inflammatory phenotype. COP1-deficient microglia markedly accelerated tau-mediated neurodegeneration in a mouse model where activated microglia play a deleterious role. Thus, COP1 is an important suppressor of pathogenic c/EBPβ-dependent gene expression programs in microglia.
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Affiliation(s)
- Ada Ndoja
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Seung-Hye Lee
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Hai Ngu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Ying-Jiun Jasmine Chen
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Luke Xie
- Department of Biomedical Imaging, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
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22
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Loth MK, Guariglia SR, Re DB, Perez J, de Paiva VN, Dziedzic JL, Chambers JW, Azzam DJ, Guilarte TR. A Novel Interaction of Translocator Protein 18 kDa (TSPO) with NADPH Oxidase in Microglia. Mol Neurobiol 2020; 57:4467-4487. [PMID: 32743737 PMCID: PMC7515859 DOI: 10.1007/s12035-020-02042-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
In the brain neuropil, translocator protein 18 kDa (TSPO) is a stress response protein that is upregulated in microglia and astrocytes in diverse central nervous system pathologies. TSPO is widely used as a biomarker of neuroinflammation in preclinical and clinical neuroimaging studies. However, there is a paucity of knowledge on the function(s) of TSPO in glial cells. In this study, we explored a putative interaction between TSPO and NADPH oxidase 2 (NOX2) in microglia. We found that TSPO associates with gp91phox and p22phox, the principal subunits of NOX2 in primary murine microglia. The association of TSPO with gp91phox and p22phox was observed using co-immunoprecipitation, confocal immunofluorescence imaging, and proximity ligation assay. We found that besides gp91phox and p22phox, voltage-dependent anion channel (VDAC) also co-immunoprecipitated with TSPO consistent with previous reports. When we compared lipopolysaccharide (LPS) stimulated microglia to vehicle control, we found that a lower amount of gp91phox and p22phox protein co-immunoprecipitated with TSPO suggesting a disruption of the TSPO-NOX2 subunits association. TSPO immuno-gold electron microscopy confirmed that TSPO is present in the outer mitochondrial membrane but it is also found in the endoplasmic reticulum (ER), mitochondria-associated ER membrane (MAM), and in the plasma membrane. TSPO localization at the MAM may represent a subcellular site where TSPO interacts with gp91phox and p22phox since the MAM is a point of communication between outer mitochondria membrane proteins (TSPO) and ER proteins (gp91phox and p22phox) where they mature and form the cytochrome b558 (Cytb558) heterodimer. We also found that an acute burst of reactive oxygen species (ROS) increased TSPO levels on the surface of microglia and this effect was abrogated by a ROS scavenger. These results suggest that ROS production may alter the subcellular distribution of TSPO. Collectively, our findings suggest that in microglia, TSPO is associated with the major NOX2 subunits gp91phox and p22phox. We hypothesize that this interaction may regulate Cytb558 formation and modulate NOX2 levels, ROS production, and redox homeostasis in microglia.
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Affiliation(s)
- Meredith K Loth
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sara R Guariglia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Diane B Re
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Juan Perez
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA
| | - Vanessa Nunes de Paiva
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA
| | - Jennifer L Dziedzic
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA
| | - Jeremy W Chambers
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA
| | - Diana J Azzam
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA
| | - Tomás R Guilarte
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
- Department of Environmental Health Sciences, Robert Stempel College of Public Health & Social Work, Florida International University, Miami, FL, 33199, USA.
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23
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Efficient allele conversion in mouse zygotes and primary cells based on electroporation of Cre protein. Methods 2020; 191:87-94. [PMID: 32717290 DOI: 10.1016/j.ymeth.2020.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 11/22/2022] Open
Abstract
Cre-loxP recombination system is a powerful tool for genome engineering. One of its applications is found in genetic mouse models that often require to induce Cre recombination in preimplantation embryos. Here, we describe a technically simple, affordable and highly efficient protocol for Cre protein delivery into mouse zygotes by electroporation. We show that electroporation based delivery of Cre has no negative impact on embryo survival and the method can be easily combined with in vitro fertilization resulting in a significantly faster generation of desired models. Lastly, we demonstrate that Cre protein electroporation is suitable for allelic conversion in primary cells derived from conditional mouse models.
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24
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Zhang J, Webster JD, Dugger DL, Goncharov T, Roose-Girma M, Hung J, Kwon YC, Vucic D, Newton K, Dixit VM. Ubiquitin Ligases cIAP1 and cIAP2 Limit Cell Death to Prevent Inflammation. Cell Rep 2020; 27:2679-2689.e3. [PMID: 31141691 DOI: 10.1016/j.celrep.2019.04.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/29/2019] [Accepted: 04/26/2019] [Indexed: 01/18/2023] Open
Abstract
Cellular inhibitor of apoptosis proteins cIAP1 and cIAP2 ubiquitinate nuclear factor κB (NF-κB)-inducing kinase (NIK) to suppress non-canonical NF-κB signaling and substrates such as receptor interacting protein kinase 1 (RIPK1) to promote cell survival. We investigate how these functions contribute to homeostasis by eliminating cIap2 from adult cIap1-deficient mice. cIAP1 and cIAP2 (cIAP1/2) deficiency causes rapid weight loss and inflammation, with aberrant cell death, indicated by cleaved caspases-3 and -8, prevalent in intestine and liver. Deletion of Casp8 and Ripk3 prevents this aberrant cell death, reduces the inflammation, and prolongs mouse survival, whereas Ripk3 loss alone offers little benefit. Residual inflammation in mice lacking cIap1/2, Casp8, and Ripk3 is reduced by inhibition of NIK. Loss of Casp8 and Mlkl (mixed lineage kinase domain-like), but not Mlkl loss alone, also prevents cIAP1/2-deficient mice from dying around embryonic day 11. Therefore, a major function of cIAP1/2 in vivo is to suppress caspase-8-dependent cell death.
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Affiliation(s)
- Jieqiong Zhang
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA
| | - Tatiana Goncharov
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jeffrey Hung
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Youngsu C Kwon
- Department of Translational Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.
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25
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Ozguldez HO, Fan R, Bedzhov I. Placental gene editing via trophectoderm-specific Tat-Cre/loxP recombination. Development 2020; 147:dev.190371. [PMID: 32541013 DOI: 10.1242/dev.190371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/05/2020] [Indexed: 11/20/2022]
Abstract
The ways in which placental defects affect embryonic development are largely overlooked because of the lack of a trophoblast-specific approach for conditional gene ablation. To tackle this, we have established a simple, fast and efficient method for trophectodermal Tat-Cre/loxP recombination. We used the natural permeability barrier in mouse blastocysts in combination with off-the-shelf Tat-Cre recombinase to achieve editing of conditional alleles in the trophoblast lineage. This direct approach enables gene function analysis during implantation and placentation in mice, thereby crucially helping to broaden our understanding of human reproduction and development.
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Affiliation(s)
- Hatice O Ozguldez
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Rui Fan
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
| | - Ivan Bedzhov
- Embryonic Self-Organization research group, Max Planck Institute for Molecular Biomedicine, Röntgenstraße 20, 48149 Münster, Germany
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26
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Kim AH, Lee S, Jeon S, Kim GT, Lee EJ, Kim D, Kim Y, Park TS. Addition of an N-Terminal Poly-Glutamate Fusion Tag Improves Solubility and Production of Recombinant TAT-Cre Recombinase in Escherichia coli. J Microbiol Biotechnol 2020; 30:109-117. [PMID: 31693834 PMCID: PMC9728232 DOI: 10.4014/jmb.1909.09028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cre recombinase is widely used to manipulate DNA sequences for both in vitro and in vivo research. Attachment of a trans-activator of transcription (TAT) sequence to Cre allows TATCre to penetrate the cell membrane, and the addition of a nuclear localization signal (NLS) helps the enzyme to translocate into the nucleus. Since the yield of recombinant TAT-Cre is limited by formation of inclusion bodies, we hypothesized that the positively charged arginine-rich TAT sequence causes the inclusion body formation, whereas its neutralization by the addition of a negatively charged sequence improves solubility of the protein. To prove this, we neutralized the positively charged TAT sequence by proximally attaching a negatively charged poly-glutamate (E12) sequence. We found that the E12 tag improved the solubility and yield of E12-TAT-NLS-Cre (E12-TAT-Cre) compared with those of TAT-NLS-Cre (TATCre) when expressed in E. coli. Furthermore, the growth of cells expressing E12-TAT-Cre was increased compared with that of the cells expressing TAT-Cre. Efficacy of the purified TATCre was confirmed by a recombination test on a floxed plasmid in a cell-free system and 293 FT cells. Taken together, our results suggest that attachment of the E12 sequence to TAT-Cre improves its solubility during expression in E. coli (possibly by neutralizing the ionic-charge effects of the TAT sequence) and consequently increases the yield. This method can be applied to the production of transducible proteins for research and therapeutic purposes.
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Affiliation(s)
- A-Hyeon Kim
- Department of Life Sciences, Gachon University, Sungnam 320, Republic of Korea
| | - Soohyun Lee
- Department of Research and Development, LumiMac, Inc., Seoul 05844, Republic of Korea
| | - Suwon Jeon
- Department of Life Sciences, Gachon University, Sungnam 320, Republic of Korea
| | - Goon-Tae Kim
- Department of Life Sciences, Gachon University, Sungnam 320, Republic of Korea
| | - Eun Jig Lee
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 0722, Republic of Korea
| | - Daham Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 0722, Republic of Korea
| | - Younggyu Kim
- Department of Research and Development, LumiMac, Inc., Seoul 05844, Republic of Korea
| | - Tae-Sik Park
- Department of Life Sciences, Gachon University, Sungnam 320, Republic of Korea,Corresponding author Phone: +82-31-750-8824 Fax: +82-31-750-8573 E-mail:
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27
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The RIPK4-IRF6 signalling axis safeguards epidermal differentiation and barrier function. Nature 2019; 574:249-253. [PMID: 31578523 DOI: 10.1038/s41586-019-1615-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/29/2019] [Indexed: 01/30/2023]
Abstract
The integrity of the mammalian epidermis depends on a balance of proliferation and differentiation in the resident population of stem cells1. The kinase RIPK4 and the transcription factor IRF6 are mutated in severe developmental syndromes in humans, and mice lacking these genes display epidermal hyperproliferation and soft-tissue fusions that result in neonatal lethality2-5. Our understanding of how these genes control epidermal differentiation is incomplete. Here we show that the role of RIPK4 in mouse development requires its kinase activity; that RIPK4 and IRF6 expressed in the epidermis regulate the same biological processes; and that the phosphorylation of IRF6 at Ser413 and Ser424 primes IRF6 for activation. Using RNA sequencing (RNA-seq), histone chromatin immunoprecipitation followed by sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) of skin in wild-type and IRF6-deficient mouse embryos, we define the transcriptional programs that are regulated by IRF6 during epidermal differentiation. IRF6 was enriched at bivalent promoters, and IRF6 deficiency caused defective expression of genes that are involved in the metabolism of lipids and the formation of tight junctions. Accordingly, the lipid composition of the stratum corneum of Irf6-/- skin was abnormal, culminating in a severe defect in the function of the epidermal barrier. Collectively, our results explain how RIPK4 and IRF6 function to ensure the integrity of the epidermis and provide mechanistic insights into why developmental syndromes that are characterized by orofacial, skin and genital abnormalities result when this axis goes awry.
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28
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FBXO7 sensitivity of phenotypic traits elucidated by a hypomorphic allele. PLoS One 2019; 14:e0212481. [PMID: 30840666 PMCID: PMC6402633 DOI: 10.1371/journal.pone.0212481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/04/2019] [Indexed: 11/19/2022] Open
Abstract
FBXO7 encodes an F box containing protein that interacts with multiple partners to facilitate numerous cellular processes and has a canonical role as part of an SCF E3 ubiquitin ligase complex. Mutation of FBXO7 is responsible for an early onset Parkinsonian pyramidal syndrome and genome-wide association studies have linked variants in FBXO7 to erythroid traits. A putative orthologue in Drosophila, nutcracker, has been shown to regulate the proteasome, and deficiency of nutcracker results in male infertility. Therefore, we reasoned that modulating Fbxo7 levels in a murine model could provide insights into the role of this protein in mammals. We used a targeted gene trap model which retained 4-16% residual gene expression and assessed the sensitivity of phenotypic traits to gene dosage. Fbxo7 hypomorphs showed regenerative anaemia associated with a shorter erythrocyte half-life, and male mice were infertile. Alterations to T cell phenotypes were also observed, which intriguingly were both T cell intrinsic and extrinsic. Hypomorphic mice were also sensitive to infection with Salmonella, succumbing to a normally sublethal challenge. Despite these phenotypes, Fbxo7 hypomorphs were produced at a normal Mendelian ratio with a normal lifespan and no evidence of neurological symptoms. These data suggest that erythrocyte survival, T cell development and spermatogenesis are particularly sensitive to Fbxo7 gene dosage.
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29
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Kim HR, Rahman FU, Kim KS, Kim EK, Cho SM, Lee K, Moon OS, Seo YW, Yoon WK, Won YS, Kang H, Kim HC, Nam KH. Critical Roles of E2F3 in Growth and Musculo-skeletal Phenotype in Mice. Int J Med Sci 2019; 16:1557-1563. [PMID: 31839743 PMCID: PMC6909802 DOI: 10.7150/ijms.39068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/11/2019] [Indexed: 12/24/2022] Open
Abstract
E2F3, a member of the E2F family, plays a critical role in cell cycle and proliferation by targeting downstream, retinoblastoma (RB) a tumor suppressor family protein. The purpose of this study, was to investigate the role and function of E2F3 in vivo. We examined phenotypic abnormalities, by deletion of the E2f3 gene in mice. Complete ablation of the E2F3 was fully penetrant, in the pure C57BL/6N background. The E2f3+/ - mouse embryo developed normally without fatal disorder. However, they exhibited reduced body weight, growth retardation, skeletal imperfection, and poor grip strength ability. Findings suggest that E2F3 has a pivotal role in muscle and bone development, and affect normal mouse growth.
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Affiliation(s)
- Hae-Rim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Faiz Ur Rahman
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Kwang-Soo Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea.,Department of Animal Science and Technology, Chung-Ang University, Seodong-daero 4726, Gyeonggi 17546, Korea
| | - Eun-Kyeung Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Sang-Mi Cho
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Kihoon Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Ok-Sung Moon
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Young-Won Seo
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Won-Kee Yoon
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Young-Suk Won
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Hoyoung Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Hyoung-Chin Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, Yeonjudanji-ro 30, Chungbuk 28116, Korea
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30
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Fisher CL, Marks H, Cho LTY, Andrews R, Wormald S, Carroll T, Iyer V, Tate P, Rosen B, Stunnenberg HG, Fisher AG, Skarnes WC. An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers. Nucleic Acids Res 2017; 45:e174. [PMID: 28981838 PMCID: PMC5716182 DOI: 10.1093/nar/gkx811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/25/2017] [Accepted: 09/04/2017] [Indexed: 11/18/2022] Open
Abstract
Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC 'knockout-first' ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60% and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion. We designed our strategy to select against re-targeting the 'knockout-first' allele and identify essential genes in ES cells, including the histone methyltransferase Setdb1. For confirmation, we exploited the flexibility of our system, enabling tamoxifen inducible conditional gene ablation while controlling for genetic background and tamoxifen effects. Setdb1 ablated ES cells exhibit severe growth inhibition, which is not rescued by exogenous Nanog expression or culturing in naive pluripotency '2i' media, suggesting that the self-renewal defect is mediated through pluripotency network independent pathways. Our strategy to generate null mutant mouse ES cells is applicable to thousands of genes and repurposes existing IKMC Intermediate Vectors.
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Affiliation(s)
- Cynthia L. Fisher
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Lily Ting-yin Cho
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Robert Andrews
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Sam Wormald
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Thomas Carroll
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Vivek Iyer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Peri Tate
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Barry Rosen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Amanda G. Fisher
- MRC London Institute of Medical Sciences and Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - William C. Skarnes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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31
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Zorzi V, Paciello F, Ziraldo G, Peres C, Mazzarda F, Nardin C, Pasquini M, Chiani F, Raspa M, Scavizzi F, Carrer A, Crispino G, Ciubotaru CD, Monyer H, Fetoni AR, M Salvatore A, Mammano F. Mouse Panx1 Is Dispensable for Hearing Acquisition and Auditory Function. Front Mol Neurosci 2017; 10:379. [PMID: 29234270 PMCID: PMC5712377 DOI: 10.3389/fnmol.2017.00379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 10/30/2017] [Indexed: 11/13/2022] Open
Abstract
Panx1 forms plasma membrane channels in brain and several other organs, including the inner ear. Biophysical properties, activation mechanisms and modulators of Panx1 channels have been characterized in detail, however the impact of Panx1 on auditory function is unclear due to conflicts in published results. To address this issue, hearing performance and cochlear function of the Panx1−/− mouse strain, the first with a reported global ablation of Panx1, were scrutinized. Male and female homozygous (Panx1−/−), hemizygous (Panx1+/−) and their wild type (WT) siblings (Panx1+/+) were used for this study. Successful ablation of Panx1 was confirmed by RT-PCR and Western immunoblotting in the cochlea and brain of Panx1−/− mice. Furthermore, a previously validated Panx1-selective antibody revealed strong immunoreactivity in WT but not in Panx1−/− cochleae. Hearing sensitivity, outer hair cell-based “cochlear amplifier” and cochlear nerve function, analyzed by auditory brainstem response (ABR) and distortion product otoacoustic emission (DPOAE) recordings, were normal in Panx1+/− and Panx1−/− mice. In addition, we determined that global deletion of Panx1 impacts neither on connexin expression, nor on gap-junction coupling in the developing organ of Corti. Finally, spontaneous intercellular Ca2+ signal (ICS) activity in organotypic cochlear cultures, which is key to postnatal development of the organ of Corti and essential for hearing acquisition, was not affected by Panx1 ablation. Therefore, our results provide strong evidence that, in mice, Panx1 is dispensable for hearing acquisition and auditory function.
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Affiliation(s)
- Veronica Zorzi
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,School of Medicine, Institute of Otolaryngology, Catholic University, Rome, Italy
| | - Fabiola Paciello
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | - Gaia Ziraldo
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,School of Medicine, Institute of Otolaryngology, Catholic University, Rome, Italy
| | - Chiara Peres
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | - Flavia Mazzarda
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Science, Roma Tre University, Rome, Italy
| | - Chiara Nardin
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Science, Roma Tre University, Rome, Italy
| | - Miriam Pasquini
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Francesco Chiani
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | - Marcello Raspa
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | | | - Andrea Carrer
- Department of Physics and Astronomy G. Galilei, University of Padua, Padua, Italy
| | - Giulia Crispino
- Department of Physics and Astronomy G. Galilei, University of Padua, Padua, Italy
| | | | - Hannah Monyer
- Department of Clinical Neurobiology, Deutches Krebforschungzentrum, University of Heidelberg, Heidelberg, Germany
| | - Anna R Fetoni
- School of Medicine, Institute of Otolaryngology, Catholic University, Rome, Italy
| | - Anna M Salvatore
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | - Fabio Mammano
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Physics and Astronomy G. Galilei, University of Padua, Padua, Italy.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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Cleavage of DFNA5 by caspase-3 during apoptosis mediates progression to secondary necrotic/pyroptotic cell death. Nat Commun 2017; 8:14128. [PMID: 28045099 PMCID: PMC5216131 DOI: 10.1038/ncomms14128] [Citation(s) in RCA: 877] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/04/2016] [Indexed: 12/29/2022] Open
Abstract
Apoptosis is a genetically regulated cell suicide programme mediated by activation of the effector caspases 3, 6 and 7. If apoptotic cells are not scavenged, they progress to a lytic and inflammatory phase called secondary necrosis. The mechanism by which this occurs is unknown. Here we show that caspase-3 cleaves the GSDMD-related protein DFNA5 after Asp270 to generate a necrotic DFNA5-N fragment that targets the plasma membrane to induce secondary necrosis/pyroptosis. Cells that express DFNA5 progress to secondary necrosis, when stimulated with apoptotic triggers such as etoposide or vesicular stomatitis virus infection, but disassemble into small apoptotic bodies when DFNA5 is deleted. Our findings identify DFNA5 as a central molecule that regulates apoptotic cell disassembly and progression to secondary necrosis, and provide a molecular mechanism for secondary necrosis. Because DFNA5-induced secondary necrosis and GSDMD-induced pyroptosis are dependent on caspase activation, we propose that they are forms of programmed necrosis. DFNA5 is related to the caspase-dependent pyroptosis inducer gasdermin D. Here the authors find that DFNA5 is cleaved by caspase 3 and show this cleavage skews cells away from apoptosis into secondary necrosis, a form of cell death characterized by membrane ballooning similar to pyroptosis.
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33
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Cambridge EL, McIntyre Z, Clare S, Arends MJ, Goulding D, Isherwood C, Caetano SS, Reviriego CB, Swiatkowska A, Kane L, Harcourt K, Adams DJ, White JK, Speak AO. The AMP-activated protein kinase beta 1 subunit modulates erythrocyte integrity. Exp Hematol 2016; 45:64-68.e5. [PMID: 27666489 PMCID: PMC5823972 DOI: 10.1016/j.exphem.2016.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 12/03/2022]
Abstract
Failure to maintain a normal in vivo erythrocyte half-life results in the development of hemolytic anemia. Half-life is affected by numerous factors, including energy balance, electrolyte gradients, reactive oxygen species, and membrane plasticity. The heterotrimeric AMP-activated protein kinase (AMPK) is an evolutionarily conserved serine/threonine kinase that acts as a critical regulator of cellular energy balance. Previous roles for the alpha 1 and gamma 1 subunits in the control of erythrocyte survival have been reported. In the work described here, we studied the role of the beta 1 subunit in erythrocytes and observed microcytic anemia with compensatory extramedullary hematopoiesis together with splenomegaly and increased osmotic resistance. Prkab1tm1b/tm1b mice were generated and phenotyped. Prkab1tm1b/tm1b mice presented with microcytic anemia. Erythrocytes lacking Prkab1 have a variable morphologic appearance. Prkab1-deficient erythrocytes have increased osmotic resistance. The importance of the beta 1 isoform in erythrocyte integrity is discussed.
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Affiliation(s)
- Emma L Cambridge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Zoe McIntyre
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Centre for Comparative Pathology, Institute of Genetics & Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - David Goulding
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Christopher Isherwood
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Susana S Caetano
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | | | - Agnieszka Swiatkowska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Leanne Kane
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Katherine Harcourt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | -
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jacqueline K White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.
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34
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Lee S, Pallerla SR, Kim S, Shaffer B, Simerly CR, Richard Chaillet J, Barak Y. Esrrb-Cre excises loxP-flanked alleles in early four-cell embryos. Genesis 2015; 54:53-61. [PMID: 26663459 DOI: 10.1002/dvg.22912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 12/03/2015] [Accepted: 12/03/2015] [Indexed: 11/06/2022]
Abstract
Among transgenic mice with ubiquitous Cre recombinase activity, all strains to date excise loxP-flanked (floxed) alleles either at or before the zygote stage or at nondescript stages of development. This manuscript describes a new mouse strain, in which Cre recombinase, integrated into the Esrrb locus, efficiently excises floxed alleles in pre-implantation embryos at the onset of the four-cell stage. By enabling inactivation of genes only after the embryo has undergone two cleavages, this strain should facilitate in vivo studies of genes with essential gametic or zygotic functions. In addition, this study describes a new, highly pluripotent hybrid C57BL/6J x 129S1/SvImJ mouse embryonic stem cell line, HYB12, in which this knockin and additional targeted alleles have been generated.
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Affiliation(s)
- Sungeun Lee
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - Srinivas R Pallerla
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - Suyeon Kim
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - Benjamin Shaffer
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - Calvin R Simerly
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - J Richard Chaillet
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
| | - Yaacov Barak
- Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, 204 Craft Ave., Pittsburgh, PA 15213
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35
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Dolatshad H, Biggs D, Diaz R, Hortin N, Preece C, Davies B. A versatile transgenic allele for mouse overexpression studies. Mamm Genome 2015; 26:598-608. [PMID: 26369329 PMCID: PMC4653235 DOI: 10.1007/s00335-015-9602-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/17/2015] [Indexed: 12/31/2022]
Abstract
For the analysis of gene function in vivo, gene overexpression in the mouse provides an alternative to loss-of-function knock-out approaches and can help reveal phenotypes where compensatory mechanisms are at play. Furthermore, when multiple lines overexpressing a gene-of-interest at varying levels are studied, the consequences of differences in gene dosage can be explored. Despite these advantages, inherent shortcomings in the methodologies used for the generation of gain-of-function transgenic mouse models have limited their application to functional gene analysis, and the necessity for multiple lines comes at a significant animal and financial cost. The targeting of transgenic overexpression constructs at single copy into neutral genomic loci is the preferred method for the generation of such models, which avoids the unpredictable outcomes associated with conventional random integration. However, despite the increased reliability that targeted transgenic methodologies provide, only one expression level results, as defined by the promoter used. Here, we report a new versatile overexpression allele, the promoter-switch allele, which couples PhiC31 integrase-targeted transgenesis with Flp recombinase promoter switching and Cre recombinase activation. These recombination switches allow the conversion of different overexpression alleles, combining the advantages of transgenic targeting with tunable transgene expression. With this approach, phenotype severity can be correlated with transgene expression in a single mouse model, providing a cost-effective solution amenable to systematic gain-of-function studies.
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Affiliation(s)
- Hamid Dolatshad
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Daniel Biggs
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Rebeca Diaz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Nicole Hortin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Christopher Preece
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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36
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Rosen B, Schick J, Wurst W. Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes. Mamm Genome 2015; 26:456-66. [PMID: 26340938 DOI: 10.1007/s00335-015-9598-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/13/2015] [Indexed: 11/29/2022]
Abstract
The International Knockout Mouse Consortium (IKMC; http://www.mousephenotype.org ) has generated mutations in almost every protein-coding mouse gene and is completing the companion Cre driver resource to expand tissue-specific conditional mutagenesis. Accordingly, the IKMC has carried out high-throughput gene trapping and targeting producing conditional mutations in murine embryonic stem cells in more than 18,500 genes, from which at least 4900 mutant mouse lines have been established to date. This resource is currently being upgraded with more powerful tools, such as visualization and manipulation cassettes that can be easily introduced into IKMC alleles for multifaceted functional studies. In addition, we discuss how existing IKMC products can be used in combination with CRISPR technology to accelerate genome engineering projects. All information and materials from this extraordinary biological resource together with coordinated phenotyping efforts can be retrieved at www.mousephenotype.org . The comprehensive IKMC knockout resource in combination with an extensive set of modular gene cassettes will continue to enhance functional gene annotation in the future and solidify its impact on biomedical research.
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Affiliation(s)
- B Rosen
- Stem Cell Engineering, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - J Schick
- German Research Center for Environmental Health, Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - W Wurst
- German Research Center for Environmental Health, Institute of Developmental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Technische Universität München-Weihenstephan, Lehrstuhl für Entwicklungsgenetik, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Standort München Feodor-Lynen Strasse 17, 81377, Munich, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen Strasse 17, 81377, Munich, Germany.
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37
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Towards a better understanding of mouse and human diseases-International Mouse Phenotyping Consortium. SCIENCE CHINA-LIFE SCIENCES 2015; 58:392-5. [PMID: 25862663 DOI: 10.1007/s11427-015-4841-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 12/15/2014] [Indexed: 10/23/2022]
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