1
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Zhao X, Zhu S, Peng W, Xue HH. The Interplay of Transcription and Genome Topology Programs T Cell Development and Differentiation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:2269-2278. [PMID: 36469845 PMCID: PMC9731349 DOI: 10.4049/jimmunol.2200625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/14/2022] [Indexed: 01/04/2023]
Abstract
T cells are essential for mounting defense against various pathogens and malignantly transformed cells. Thymic development and peripheral T cell differentiation are highly orchestrated biological processes that require precise gene regulation. Higher-order genome organization on multiple scales, in the form of chromatin loops, topologically associating domains and compartments, provides pivotal control of T cell gene expression. CTCF and the cohesin machinery are ubiquitously expressed architectural proteins responsible for establishing chromatin structures. Recent studies indicate that transcription factors, such as T lineage-defining Tcf1 and TCR-induced Batf, may have intrinsic ability and/or engage CTCF to shape chromatin architecture. In this article, we summarize current knowledge on the dynamic changes in genome topology that underlie normal or leukemic T cell development, CD4+ helper T cell differentiation, and CD8+ cytotoxic T cell functions. The knowledge lays a solid foundation for elucidating the causative link of spatial chromatin configuration to transcriptional and functional output in T cells.
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Affiliation(s)
- Xin Zhao
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
| | - Shaoqi Zhu
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington DC, 20052
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ 07110
- New Jersey Veterans Affairs Health Care System, East Orange, NJ 07018
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2
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Chatenoud L, Marquet C, Valette F, Scott L, Quan J, Bu CH, Hildebrand S, Moresco EMY, Bach JF, Beutler B. Modulation of autoimmune diabetes by N-ethyl-N-nitrosourea- induced mutations in non-obese diabetic mice. Dis Model Mech 2022; 15:275575. [PMID: 35502705 PMCID: PMC9178510 DOI: 10.1242/dmm.049484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
Genetic association studies of type 1 diabetes (T1D) in humans, and in congenic non-obese diabetic (NOD) mice harboring DNA segments from T1D-resistant mice, face the challenge of assigning causation to specific gene variants among many within loci that affect disease risk. Here, we created random germline mutations in NOD/NckH mice and used automated meiotic mapping to identify mutations modifying T1D incidence and age of onset. In contrast with association studies in humans or congenic NOD mice, we analyzed a relatively small number of genetic changes in each pedigree, permitting implication of specific mutations as causative. Among 844 mice from 14 pedigrees bearing 594 coding/splicing changes, we identified seven mutations that accelerated T1D development, and five that delayed or suppressed T1D. Eleven mutations affected genes not previously known to influence T1D (Xpnpep1, Herc1, Srrm2, Rapgef1, Ppl, Zfp583, Aldh1l1, Col6a1, Ccdc13, Cd200r1, Atrnl1). A suppressor mutation in Coro1a validated the screen. Mutagenesis coupled with automated meiotic mapping can detect genes in which allelic variation influences T1D susceptibility in NOD mice. Variation of some of the orthologous/paralogous genes may influence T1D susceptibility in humans.
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Affiliation(s)
- Lucienne Chatenoud
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Cindy Marquet
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Fabrice Valette
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jean-François Bach
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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3
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Ikegami H, Babaya N, Noso S. β-Cell failure in diabetes: Common susceptibility and mechanisms shared between type 1 and type 2 diabetes. J Diabetes Investig 2021; 12:1526-1539. [PMID: 33993642 PMCID: PMC8409822 DOI: 10.1111/jdi.13576] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/24/2022] Open
Abstract
Diabetes mellitus is etiologically classified into type 1, type 2 and other types of diabetes. Despite distinct etiologies and pathogenesis of these subtypes, many studies have suggested the presence of shared susceptibilities and underlying mechanisms in β-cell failure among different types of diabetes. Understanding these susceptibilities and mechanisms can help in the development of therapeutic strategies regardless of the diabetes subtype. In this review, we discuss recent evidence indicating the shared genetic susceptibilities and common molecular mechanisms between type 1, type 2 and other types of diabetes, and highlight the future prospects as well.
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Affiliation(s)
- Hiroshi Ikegami
- Department of Endocrinology, Metabolism and DiabetesFaculty of MedicineKindai UniversityOsaka‐sayama, OsakaJapan
| | - Naru Babaya
- Department of Endocrinology, Metabolism and DiabetesFaculty of MedicineKindai UniversityOsaka‐sayama, OsakaJapan
| | - Shinsuke Noso
- Department of Endocrinology, Metabolism and DiabetesFaculty of MedicineKindai UniversityOsaka‐sayama, OsakaJapan
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4
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Genetic Variation in Type 1 Diabetes Reconfigures the 3D Chromatin Organization of T Cells and Alters Gene Expression. Immunity 2020; 52:257-274.e11. [PMID: 32049053 DOI: 10.1016/j.immuni.2020.01.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/23/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Genetics is a major determinant of susceptibility to autoimmune disorders. Here, we examined whether genome organization provides resilience or susceptibility to sequence variations, and how this would contribute to the molecular etiology of an autoimmune disease. We generated high-resolution maps of linear and 3D genome organization in thymocytes of NOD mice, a model of type 1 diabetes (T1D), and the diabetes-resistant C57BL/6 mice. Multi-enhancer interactions formed at genomic regions harboring genes with prominent roles in T cell development in both strains. However, diabetes risk-conferring loci coalesced enhancers and promoters in NOD, but not C57BL/6 thymocytes. 3D genome mapping of NODxC57BL/6 F1 thymocytes revealed that genomic misfolding in NOD mice is mediated in cis. Moreover, immune cells infiltrating the pancreas of humans with T1D exhibited increased expression of genes located on misfolded loci in mice. Thus, genetic variation leads to altered 3D chromatin architecture and associated changes in gene expression that may underlie autoimmune pathology.
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5
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Abstract
There are now a number of different mouse models for type 1 diabetes. The best known is the nonobese diabetic (NOD) mouse which has a genetic susceptibility to autoimmune diabetes with some features that are similar to human type 1 diabetes. The mice also have a propensity to other autoimmune diatheses, including autoimmune thyroid disease and sialadenitis. In addition, it is well known that environmental factors affect the incidence of disease in these mice. While there are other rodent models, including numerous transgenic and knockout models, as well as those that express human proteins, none of these develop spontaneous diabetes over a period of time, when the natural history can be studied. We focus here on the unmanipulated NOD mouse and discuss features of the husbandry and investigation of the mice that allow for use of these long-studied mice in the pathogenesis of an autoimmune type of diabetes.
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6
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Franks SE, Getahun A, Cambier JC. A Precision B Cell-Targeted Therapeutic Approach to Autoimmunity Caused by Phosphatidylinositol 3-Kinase Pathway Dysregulation. THE JOURNAL OF IMMUNOLOGY 2019; 202:3381-3393. [PMID: 31076529 DOI: 10.4049/jimmunol.1801394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/08/2019] [Indexed: 12/17/2022]
Abstract
The inositol lipid phosphatases PTEN and SHIP-1 play a crucial role in maintaining B cell anergy and are reduced in expression in B cells from systemic lupus erythematosus and type 1 diabetes patients, consequent to aberrant regulation by miRNA-7 and 155. With an eye toward eventual use in precision medicine therapeutic approaches in autoimmunity, we explored the ability of p110δ inhibition to compensate for PI3K pathway dysregulation in mouse models of autoimmunity. Low dosages of the p110δ inhibitor idelalisib, which spare the ability to mount an immune response to exogenous immunogens, are able to block the development of autoimmunity driven by compromised PI3K pathway regulation resultant from acutely induced B cell-targeted haploinsufficiency of PTEN and SHIP-1. These conditions do not block autoimmunity driven by B cell loss of the regulatory tyrosine phosphatase SHP-1. Finally, we show that B cells in NOD mice express reduced PTEN, and low-dosage p110δ inhibitor therapy blocks disease progression in this model of type 1 diabetes. These studies may aid in the development of precision treatments that act by enforcing PI3K pathway regulation in patients carrying specific risk alleles.
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Affiliation(s)
- S Elizabeth Franks
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Andrew Getahun
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
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7
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Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J. Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med 2017; 9:49. [PMID: 28558813 PMCID: PMC5448149 DOI: 10.1186/s13073-017-0441-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.
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Affiliation(s)
- Charles A Steward
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK. .,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | | | - Berge A Minassian
- Department of Pediatrics (Neurology), University of Texas Southwestern, Dallas, TX, USA.,Program in Genetics and Genome Biology and Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, WC1N 3BG, UK.,Chalfont Centre for Epilepsy, Chesham Lane, Chalfont St Peter, Buckinghamshire, SL9 0RJ, UK
| | - Adam Frankish
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Illumina Inc, Great Chesterford, Essex, CB10 1XL, UK
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8
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Zhang Q, Chikina M, Szymczak-Workman AL, Horne W, Kolls JK, Vignali KM, Normolle D, Bettini M, Workman CJ, Vignali DAA. LAG3 limits regulatory T cell proliferation and function in autoimmune diabetes. Sci Immunol 2017; 2:2/9/eaah4569. [PMID: 28783703 DOI: 10.1126/sciimmunol.aah4569] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/18/2016] [Accepted: 02/14/2017] [Indexed: 01/19/2023]
Abstract
Inhibitory receptors (IRs) are pivotal in controlling T cell homeostasis because of their intrinsic regulation of conventional effector T (Tconv) cell proliferation, viability, and function. However, the role of IRs on regulatory T cells (Tregs) remains obscure because they could be required for suppressive activity and/or limit Treg function. We evaluated the role of lymphocyte activation gene 3 (LAG3; CD223) on Tregs by generating mice in which LAG3 is absent on the cell surface of Tregs in a murine model of type 1 diabetes. Unexpectedly, mice that lacked LAG3 expression on Tregs exhibited reduced autoimmune diabetes, consistent with enhanced Treg proliferation and function. Whereas the transcriptional landscape of peripheral wild-type (WT) and Lag3-deficient Tregs was largely comparable, substantial differences between intra-islet Tregs were evident and involved a subset of genes and pathways that promote Treg maintenance and function. Consistent with these observations, Lag3-deficient Tregs outcompeted WT Tregs in the islets but not in the periphery in cotransfer experiments because of enhanced interleukin-2-signal transducer and activator of transcription 5 signaling and increased Eos expression. Our study suggests that LAG3 intrinsically limits Treg proliferation and function at inflammatory sites, promotes autoimmunity in a chronic autoimmune-prone environment, and may contribute to Treg insufficiency in autoimmune disease.
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Affiliation(s)
- Qianxia Zhang
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Andrea L Szymczak-Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - William Horne
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Jay K Kolls
- Richard King Mellon Foundation Institute for Pediatric Research, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Kate M Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Daniel Normolle
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Maria Bettini
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA. .,Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Tumor Microenvironment Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
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9
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Abstract
Type 1 diabetes (T1D) results from a chronic and selective destruction of insulin-secreting β-cells within the islets of Langerhans of the pancreas by autoreactive CD4(+) and CD8(+) T lymphocytes. The use of animal models of T1D was instrumental for deciphering the steps of the autoimmune process leading to T1D. The non-obese diabetic (NOD) mouse and the bio-breeding (BB) rat spontaneously develop the disease similar to the human pathology in terms of the immune responses triggering autoimmune diabetes and of the genetic and environmental factors influencing disease susceptibility. The generation of genetically modified models allowed refining our understanding of the etiology and the pathogenesis of the disease. In the present review, we provide an overview of the experimental models generated and used to gain knowledge on the molecular and cellular mechanisms underlying the breakdown of self-tolerance in T1D and the progression of the autoimmune response. Immunotherapeutic interventions designed in these animal models and translated into the clinical arena in T1D patients will also be discussed.
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10
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Mudge JM, Harrow J. Creating reference gene annotation for the mouse C57BL6/J genome assembly. Mamm Genome 2015; 26:366-78. [PMID: 26187010 PMCID: PMC4602055 DOI: 10.1007/s00335-015-9583-x] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/18/2015] [Indexed: 12/14/2022]
Abstract
Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. Initially, the principle focus was on the identification of all protein-coding genes, although today the importance of describing long non-coding RNAs, small RNAs, and pseudogenes is recognized. Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico validation pipelines from other members of the consortium. We discuss the more recent incorporation of next-generation sequencing datasets into this workflow, including the usage of mass-spectrometry data to potentially identify novel protein-coding genes. Finally, we will outline how the C57BL6/J genebuild can be used to gain insights into the variant sites that distinguish different mouse strains and species.
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11
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Lebailly B, Boitard C, Rogner UC. Circadian rhythm-related genes: implication in autoimmunity and type 1 diabetes. Diabetes Obes Metab 2015; 17 Suppl 1:134-8. [PMID: 26332978 DOI: 10.1111/dom.12525] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 05/05/2015] [Indexed: 01/11/2023]
Abstract
Recent gene association and functional studies have proven the implication of several circadian rhythm-related genes in diabetes. Diabetes has been related to variation in central circadian regulation and peripheral oscillation. Different transcriptional regulators have been identified. Circadian genes are clearly implicated in metabolic pathways, pancreatic function and in type 2 diabetes. Much less evidence has been shown for the link between circadian regulation and type 1 diabetes. The hypothesis that circadian genes are involved in type 1 diabetes is reinforced by findings that the immune system undergoes circadian variation and that several autoimmune diseases are associated with circadian genes. Recent findings in the non-obese diabetic mouse model pinpoint to specific mechanisms controlling type 1 diabetes by the clock-related gene Arntl2 in the immune system.
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Affiliation(s)
- B Lebailly
- Institut Cochin (INSERM U1016, CNRS UMR-S8104, Département "Endocrinologie, Métabolisme et Diabètes), Paris, France
- Cellule Pasteur, University Pierre and Marie Curie, Paris, France
| | - C Boitard
- Institut Cochin (INSERM U1016, CNRS UMR-S8104, Département "Endocrinologie, Métabolisme et Diabètes), Paris, France
| | - U C Rogner
- Institut Cochin (INSERM U1016, CNRS UMR-S8104, Département "Endocrinologie, Métabolisme et Diabètes), Paris, France
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12
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Adams DJ, Doran AG, Lilue J, Keane TM. The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes. Mamm Genome 2015; 26:403-12. [PMID: 26123534 DOI: 10.1007/s00335-015-9579-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/11/2015] [Indexed: 12/16/2022]
Abstract
The Mouse Genomes Project was initiated in 2009 with the goal of using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion/deletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project's website ( http://www.sanger.ac.uk/resources/mouse/genomes/ ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics.
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Affiliation(s)
- David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.
| | - Anthony G Doran
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.
| | - Jingtao Lilue
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.
| | - Thomas M Keane
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK.
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13
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Motta VN, Markle JGM, Gulban O, Mortin-Toth S, Liao KC, Mogridge J, Steward CA, Danska JS. Identification of the inflammasome Nlrp1b as the candidate gene conferring diabetes risk at the Idd4.1 locus in the nonobese diabetic mouse. THE JOURNAL OF IMMUNOLOGY 2015; 194:5663-73. [PMID: 25964492 DOI: 10.4049/jimmunol.1400913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 04/13/2015] [Indexed: 11/19/2022]
Abstract
Type 1 diabetes in the NOD mouse model has been linked to >30 insulin-dependent diabetes (Idd) susceptibility loci. Idd4 on chromosome 11 consists of two subloci, Idd4.1 and Idd4.2. Using congenic analysis of alleles in NOD and NOD-resistant (NOR) mice, we previously defined Idd4.1 as an interval containing >50 genes that controlled expression of genes in the type 1 IFN pathway. In this study, we report refined mapping of Idd4.1 to a 1.1-Mb chromosomal region and provide genomic sequence analysis and mechanistic evidence supporting its role in innate immune regulation of islet-directed autoimmunity. Genetic variation at Idd4.1 was mediated by radiation-sensitive hematopoietic cells, and type 1 diabetes protection conferred by the NOR allele was abrogated in mice treated with exogenous type 1 IFN-β. Next generation sequence analysis of the full Idd4.1 genomic interval in NOD and NOR strains supported Nlrp1b as a strong candidate gene for Idd4.1. Nlrp1b belongs to the Nod-like receptor (NLR) gene family and contributes to inflammasome assembly, caspase-1 recruitment, and release of IL-1β. The Nlrp1b of NOR was expressed as an alternative spliced isoform that skips exon 9, resulting in a premature stop codon predicted to encode a truncated protein. Functional analysis of the truncated NOR Nlrp1b protein demonstrated that it was unable to recruit caspase-1 and process IL-1β. Our data suggest that Idd4.1-dependent protection from islet autoimmunity is mediated by differences in type 1 IFN- and IL-1β-dependent immune responses resulting from genetic variation in Nlrp1b.
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Affiliation(s)
- Vinicius N Motta
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Janet G M Markle
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Omid Gulban
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Steven Mortin-Toth
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Kuo-Chien Liao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jeremy Mogridge
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Charles A Steward
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom; and
| | - Jayne S Danska
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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14
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Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG. The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res 2013; 42:D771-9. [PMID: 24316575 PMCID: PMC3964964 DOI: 10.1093/nar/gkt1241] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.uk), initially designed as a community resource for browsing manual annotation of the human genome project, now contains five reference genomes (human, mouse, zebrafish, pig and rat). Its introduction pages have been redesigned to enable the user to easily navigate between whole genomes and smaller multi-species haplotypic regions of interest such as the major histocompatibility complex. The VEGA browser is unique in that annotation is updated via the Human And Vertebrate Analysis aNd Annotation (HAVANA) update track every 2 weeks, allowing single gene updates to be made publicly available to the research community quickly. The user can now access different haplotypic subregions more easily, such as those from the non-obese diabetic mouse, and display them in a more intuitive way using the comparative tools. We also highlight how the user can browse manually annotated updated patches from the Genome Reference Consortium (GRC).
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Affiliation(s)
- Jennifer L Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK
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