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Shiina T, Kulski JK. HLA Genetics for the Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:237-258. [PMID: 38467984 DOI: 10.1007/978-981-99-9781-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes. Next generation sequencing (NGS) technology developed in recent years has provided breakthroughs in various HLA genomic/gene studies and transplant medicine. In this chapter, we review the current information on the HLA genomic structure and polymorphisms, as well as the genetic context in which numerous disease associations have been identified in this region.
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Affiliation(s)
| | - Jerzy K Kulski
- Tokai University School of Medicine, Isehara, Japan
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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Wimalarathne MM, Wilkerson-Vidal QC, Hunt EC, Love-Rutledge ST. The case for FAT10 as a novel target in fatty liver diseases. Front Pharmacol 2022; 13:972320. [PMID: 36386217 PMCID: PMC9665838 DOI: 10.3389/fphar.2022.972320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2022] [Indexed: 12/13/2022] Open
Abstract
Human leukocyte antigen F locus adjacent transcript 10 (FAT10) is a ubiquitin-like protein that targets proteins for degradation. TNFα and IFNγ upregulate FAT10, which increases susceptibility to inflammation-driven diseases like nonalcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and hepatocellular carcinoma (HCC). It is well established that inflammation contributes to fatty liver disease, but how inflammation contributes to upregulation and what genes are involved is still poorly understood. New evidence shows that FAT10 plays a role in mitophagy, autophagy, insulin signaling, insulin resistance, and inflammation which may be directly associated with fatty liver disease development. This review will summarize the current literature regarding FAT10 role in developing liver diseases and potential therapeutic targets for nonalcoholic/alcoholic fatty liver disease and hepatocellular carcinoma.
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Nyaga DM, Vickers MH, Jefferies C, Perry JK, O'Sullivan JM. The genetic architecture of type 1 diabetes mellitus. Mol Cell Endocrinol 2018; 477:70-80. [PMID: 29913182 DOI: 10.1016/j.mce.2018.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/14/2018] [Accepted: 06/06/2018] [Indexed: 02/07/2023]
Abstract
Type 1 diabetes mellitus (T1D) is a complex autoimmune disorder characterised by loss of the insulin-producing pancreatic beta cells in genetically predisposed individuals, ultimately resulting in insulin deficiency and hyperglycaemia. T1D is most common among children and young adults, and the incidence is on the rise across the world. The aetiology of T1D is hypothesized to involve genetic and environmental factors that result in the T-cell mediated destruction of pancreatic beta cells. There is a strong genetic risk to T1D; with genome-wide association studies (GWAS) identifying over 60 susceptibility regions within the human genome which are marked by single nucleotide polymorphisms (SNPs). Here, we review what is currently known about the genetics of T1D. We argue that advancing our understanding of the aetiology and pathogenesis of T1D will require the integration of genome biology (omics-data) with GWAS data, thereby making it possible to elucidate the putative gene regulatory networks modulated by disease-associated SNPs. This approach has a potential to revolutionize clinical management of T1D in an era of precision medicine.
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Affiliation(s)
- Denis M Nyaga
- The Liggins Institute, The University of Auckland, New Zealand
| | - Mark H Vickers
- The Liggins Institute, The University of Auckland, New Zealand
| | - Craig Jefferies
- The Liggins Institute, The University of Auckland, New Zealand; Starship Children's Health, Auckland, New Zealand
| | - Jo K Perry
- The Liggins Institute, The University of Auckland, New Zealand
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Gerasimou P, Skordis N, Picolos M, Spyridonidis A, Costeas P. HLA-G 14-bp polymorphism affects the age of onset in Type I Diabetes Mellitus. Int J Immunogenet 2016; 43:135-42. [PMID: 27080982 DOI: 10.1111/iji.12259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/02/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023]
Abstract
Type I diabetes mellitus (T1DM) is an organ-specific autoimmune disorder affecting the insulin-producing pancreatic cells. T1DM genetic association studies have so far revealed the involvement of more than 40 loci, with particularly strong associations for the human leucocyte antigens (HLA). Further to the well-established HLA class II associations, the immunomodulatory elements in the telomeric major histocompatibility complex locus, specifically nonclassical HLA class I, were also associated with T1DM, either in conferring susceptibility or by contributing to the overall pathogenesis. This study investigates the involvement of a 14-bp deletion polymorphism (rs371194629) at the 3' untranslated region of HLA-G in the context of T1DM and age of onset. The frequency of the polymorphism was determined in unrelated T1DM Cypriot patients and findings that emerge from this study show a strong association between the HLA-G 14-bp polymorphism and T1DM with respect to the age of onset. Specifically, the deletion/deletion (DEL/DEL) genotype was found to be associated with an early age of onset (P = 0.001), while the presence of the insertion allele (INS) was associated to a later age of onset (P = 0.0001), portraying a possible dominant effect over the deletion allele, a role in delaying disease onset and an overall involvement of HLA-G in the pathogenesis of type I diabetes mellitus.
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Affiliation(s)
- P Gerasimou
- Karaiskakio Foundation, Nicosia, Cyprus.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - N Skordis
- Division of Paediatric Endocrinology, Paedi Centre for Specialized Paediatrics, Nicosia, Cyprus
| | - M Picolos
- Alithia Endocrinology Centre, Nicosia, Cyprus
| | - A Spyridonidis
- Division of Hematology/BMT Unit, University Hospital of Patras (PGNP), Rio, Greece
| | - P Costeas
- Karaiskakio Foundation, Nicosia, Cyprus
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Brozzi F, Gerlo S, Grieco FA, Juusola M, Balhuizen A, Lievens S, Gysemans C, Bugliani M, Mathieu C, Marchetti P, Tavernier J, Eizirik DL. Ubiquitin D Regulates IRE1α/c-Jun N-terminal Kinase (JNK) Protein-dependent Apoptosis in Pancreatic Beta Cells. J Biol Chem 2016; 291:12040-56. [PMID: 27044747 DOI: 10.1074/jbc.m115.704619] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Indexed: 12/11/2022] Open
Abstract
Pro-inflammatory cytokines contribute to pancreatic beta cell apoptosis in type 1 diabetes at least in part by inducing endoplasmic reticulum (ER) stress and the consequent unfolded protein response (UPR). It remains to be determined what causes the transition from "physiological" to "apoptotic" UPR, but accumulating evidence indicates that signaling by the ER transmembrane protein IRE1α is critical for this transition. IRE1α activation is regulated by both intra-ER and cytosolic cues. We evaluated the role for the presently discovered cytokine-induced and IRE1α-interacting protein ubiquitin D (UBD) on the regulation of IRE1α and its downstream targets. UBD was identified by use of a MAPPIT (mammalian protein-protein interaction trap)-based IRE1α interactome screen followed by comparison against functional genomic analysis of human and rodent beta cells exposed to pro-inflammatory cytokines. Knockdown of UBD in human and rodent beta cells and detailed signal transduction studies indicated that UBD modulates cytokine-induced UPR/IRE1α activation and apoptosis. UBD expression is induced by the pro-inflammatory cytokines interleukin (IL)-1β and interferon (IFN)-γ in rat and human pancreatic beta cells, and it is also up-regulated in beta cells of inflamed islets from non-obese diabetic mice. UBD interacts with IRE1α in human and rodent beta cells, modulating IRE1α-dependent activation of JNK and cytokine-induced apoptosis. Our data suggest that UBD provides a negative feedback on cytokine-induced activation of the IRE1α/JNK pro-apoptotic pathway in cytokine-exposed beta cells.
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Affiliation(s)
- Flora Brozzi
- From the ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Sarah Gerlo
- the Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), 9000 Ghent, Belgium, the Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Fabio Arturo Grieco
- From the ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Matilda Juusola
- From the ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Alexander Balhuizen
- From the ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Sam Lievens
- the Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), 9000 Ghent, Belgium, the Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Conny Gysemans
- the Laboratory of Clinical and Experimental Endocrinology, KULeuven, 3000 Leuven, Belgium, and
| | - Marco Bugliani
- the Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56126 Pisa, Italy
| | - Chantal Mathieu
- the Laboratory of Clinical and Experimental Endocrinology, KULeuven, 3000 Leuven, Belgium, and
| | - Piero Marchetti
- the Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, 56126 Pisa, Italy
| | - Jan Tavernier
- the Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), 9000 Ghent, Belgium, the Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Décio L Eizirik
- From the ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium,
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Xie Z, Chang C, Zhou Z. Molecular Mechanisms in Autoimmune Type 1 Diabetes: a Critical Review. Clin Rev Allergy Immunol 2014; 47:174-92. [DOI: 10.1007/s12016-014-8422-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cort L, Habib M, Eberwine RA, Hessner MJ, Mordes JP, Blankenhorn EP. Diubiquitin (Ubd) is a susceptibility gene for virus-triggered autoimmune diabetes in rats. Genes Immun 2014; 15:168-75. [PMID: 24452267 PMCID: PMC4260472 DOI: 10.1038/gene.2013.72] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/13/2013] [Accepted: 12/03/2013] [Indexed: 12/15/2022]
Abstract
Genetic studies of type 1 diabetes (T1D) have been advanced by comparative analysis of multiple susceptible and resistant rat strains with a permissive class II MHC haplotype, RT1(u). LEW.1WR1 (but not resistant LEW.1W or WF) rats are susceptible to T1D induced by a TLR3 agonist polyinosinic:polycytidylic acid followed by infection with parvovirus. We have mapped genetic loci for virus-induced T1D susceptibility, identifying a major susceptibility locus (Iddm37) near the MHC. The Iddm37 homologs on mouse and human chromosomes are also diabetes linked. We report that a major effect gene within Iddm37 is diubiquitin (Ubd). Gene expression profiling of pancreatic lymph nodes in susceptible and resistant rats during disease induction showed differences in Ubd transcript abundance. The LEW.1WR1 Ubd promoter allele leads to higher inducible levels of UBD than that of LEW.1W or WF. Using zinc-finger nucleases , we deleted a segment of the LEW.1WR1 Ubd gene and eliminated its expression. UBD-deficient rats show substantially reduced diabetes after viral infection. Complementary studies show that there may be another diabetes gene in addition to Ubd in the Iddm37 interval. These data prove that Ubd is a diabetes susceptibility gene, providing insight into the interplay of multiple genes and environmental factors in T1D susceptibility.
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Affiliation(s)
- L Cort
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - M Habib
- Department of Medicine/Endocrinology, University of Massachusetts Medical School, Worcester, MA, USA
| | - R A Eberwine
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - M J Hessner
- Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI, USA
| | - J P Mordes
- Department of Medicine/Endocrinology, University of Massachusetts Medical School, Worcester, MA, USA
| | - E P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
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Abstract
PURPOSE OF REVIEW Recent identification of over 60 loci contributing to the susceptibility of developing type 1 diabetes (T1D) provides a timely opportunity to assess what is currently known of the genetics of T1D, and what these discoveries may tell us about the disease itself. RECENT FINDINGS The major findings will be discussed under five main themes: T1D risk gene identification, molecular mechanisms of susceptibility, shared genetic cause with other diseases, development of novel analytical methods, and understanding disease heterogeneity. SUMMARY The plethora of T1D risk genes that have been identified risk overwhelming clinicians with lists of gene names and symbols that have little bearing on management, and provide a challenge for researchers to place the genetics of T1D in a more amenable clinical context.
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Affiliation(s)
- Grant Morahan
- Centre for Diabetes Research, The Western Australian Institute for Medical Research, University of Western Australia, Perth, Western Australia, Australia.
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