Expression level of risk genes of MHC class II is a susceptibility factor for autoimmunity: New insights
Tài liệu tham khảo
Fernando, 2008, Defining the role of the MHC in autoimmunity: a review and pooled analysis, PLoS Genet., 4, 10.1371/journal.pgen.1000024
Gutierrez-Arcelus, 2016, Autoimmune diseases - connecting risk alleles with molecular traits of the immune system, Nat. Rev. Genet., 17, 160, 10.1038/nrg.2015.33
Trowsdale, 2013, Major histocompatibility complex genomics and human disease, Annu. Rev. Genom. Hum. Genet., 14, 301, 10.1146/annurev-genom-091212-153455
Miyadera, 2015, Associations of human leukocyte antigens with autoimmune diseases: challenges in identifying the mechanism, J. Hum. Genet., 60, 697, 10.1038/jhg.2015.100
Seldin, 2015, The genetics of human autoimmune disease: a perspective on progress in the field and future directions, J. Autoimmun., 64, 1, 10.1016/j.jaut.2015.08.015
Withoff, 2016, Understanding celiac disease by genomics, Trends Genet., 32, 295, 10.1016/j.tig.2016.02.003
Noble, 2015, Immunogenetics of type 1 diabetes: a comprehensive review, J. Autoimmun., 64, 101, 10.1016/j.jaut.2015.07.014
Unanue, 2016, The secrets of the class II MHC peptidome start to Be revealed, J. Immunol., 196, 939, 10.4049/jimmunol.1502571
Stern, 1994, Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide, Nature, 368, 215, 10.1038/368215a0
Henderson, 2007, The production and crystallization of the human leukocyte antigen class II molecules HLA-DQ2 and HLA-DQ8 complexed with deamidated gliadin peptides implicated in coeliac disease, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 63, 1021, 10.1107/S1744309107051408
Paul, 2013, Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource, Clin. Dev. Immunol., 2013, 467852, 10.1155/2013/467852
Shao, 2017, The SysteMHC Atlas project, Nucleic Acids Res., 45
Camarca, 2012, Repertoire of gluten peptides active in celiac disease patients: perspectives for translational therapeutic applications, Endocr. Metab. Immune Disord. Drug Targets, 12, 207, 10.2174/187153012800493549
Jabri, 2017, T cells in celiac disease, J. Immunol., 198, 3005, 10.4049/jimmunol.1601693
Molberg, 1998, Tissue transglutaminase selectively modifies gliadin peptides that are recognized by gut-derived T cells in celiac disease, Nat. Med., 4, 713, 10.1038/nm0698-713
van de Wal, 1998, Selective deamidation by tissue transglutaminase strongly enhances gliadin-specific T cell reactivity, J. Immunol., 161, 1585, 10.4049/jimmunol.161.4.1585
Vader, 2002, Specificity of tissue transglutaminase explains cereal toxicity in celiac disease, J. Exp. Med., 195, 643, 10.1084/jem.20012028
Sollid, 2012, Nomenclature and listing of celiac disease relevant gluten T-cell epitopes restricted by HLA-DQ molecules, Immunogenetics, 64, 455, 10.1007/s00251-012-0599-z
Viken, 2017, HLA class II alleles in Norwegian patients with coexisting type 1 diabetes and celiac disease, HLA, 89, 278, 10.1111/tan.12986
Cohn, 2014, Type 1 diabetes and celiac disease: clinical overlap and new insights into disease pathogenesis, Curr Diab Rep, 14, 517, 10.1007/s11892-014-0517-x
Antvorskov, 2014, Dietary gluten and the development of type 1 diabetes, Diabetologia, 57, 1770, 10.1007/s00125-014-3265-1
Serena, 2015, The role of gluten in celiac disease and type 1 diabetes, Nutrients, 7, 7143, 10.3390/nu7095329
van Lummel, 2014, Posttranslational modification of HLA-DQ binding islet autoantigens in type 1 diabetes, Diabetes, 63, 237, 10.2337/db12-1214
Matzaraki, 2017, The MHC locus and genetic susceptibility to autoimmune and infectious diseases, Genome Biol., 18, 76, 10.1186/s13059-017-1207-1
de Bakker, 2012, Interrogating the major histocompatibility complex with high-throughput genomics, Hum. Mol. Genet., 21, R29, 10.1093/hmg/dds384
Raychaudhuri, 2012, Autoimmunity: insights from human genomics, Curr. Opin. Immunol., 24, 513, 10.1016/j.coi.2012.09.006
Jia, 2013, Imputing amino acid polymorphisms in human leukocyte antigens, PLoS One, 8
Gutierrez-Achury, 2015, Fine mapping in the MHC region accounts for 18% additional genetic risk for celiac disease, Nat. Genet., 47, 577, 10.1038/ng.3268
Romanos, 2014, Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants, Gut, 63, 415, 10.1136/gutjnl-2012-304110
Lenz, 2015, Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases, Nat. Genet., 47, 1085, 10.1038/ng.3379
Hu, 2015, Additive and interaction effects at three amino acid positions in HLA-DQ and HLA-DR molecules drive type 1 diabetes risk, Nat. Genet., 47, 898, 10.1038/ng.3353
Handunnetthi, 2010, Regulation of major histocompatibility complex class II gene expression, genetic variation and disease, Gene Immun., 11, 99, 10.1038/gene.2009.83
Suzuki, 2017, Histone acetylation and the regulation of major histocompatibility class II gene expression, Adv Protein Chem. Struct. Biol., 106, 71, 10.1016/bs.apcsb.2016.08.002
Ting, 2002, Genetic control of MHC class II expression, Cell, 109, S21, 10.1016/S0092-8674(02)00696-7
Reith, 2005, Regulation of MHC class II gene expression by the class II transactivator, Nat. Rev. Immunol., 5, 793, 10.1038/nri1708
Rybtsova, 2007, Transcription-coupled deposition of histone modifications during MHC class II gene activation, Nucleic Acids Res., 35, 3431, 10.1093/nar/gkm214
Cycon, 2013, Histone deacetylase inhibitors activate CIITA and MHC class II antigen expression in diffuse large B-cell lymphoma, Immunology, 140, 259, 10.1111/imm.12136
Gomez, 2005, X box-like sequences in the MHC class II region maintain regulatory function, J. Immunol., 175, 1030, 10.4049/jimmunol.175.2.1030
Scharer, 2015, Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment, Nucleic Acids Res., 43, 3128, 10.1093/nar/gkv182
Raj, 2016, Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity, Elife, 5, 10.7554/eLife.12089
Cuddapah, 2009, Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains, Genome Res., 19, 24, 10.1101/gr.082800.108
Kim, 2015, CTCF as a multifunctional protein in genome regulation and gene expression, Exp. Mol. Med., 47, 10.1038/emm.2015.33
Majumder, 2006, The human major histocompatibility complex class II HLA-DRB1 and HLA-DQA1 genes are separated by a CTCF-binding enhancer-blocking element, J. Biol. Chem., 281, 18435, 10.1074/jbc.M601298200
Majumder, 2008, The insulator factor CTCF controls MHC class II gene expression and is required for the formation of long-distance chromatin interactions, J. Exp. Med., 205, 785, 10.1084/jem.20071843
Majumder, 2010, CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus, Mol. Cell Biol., 30, 4211, 10.1128/MCB.00327-10
Ottaviani, 2012, CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma, Nucleic Acids Res., 40, 5262, 10.1093/nar/gks158
Majumder, 2011, Cohesin regulates MHC class II genes through interactions with MHC class II insulators, J. Immunol., 187, 4236, 10.4049/jimmunol.1100688
Choi, 2011, Regulation of major histocompatibility complex class II genes, Curr. Opin. Immunol., 23, 81, 10.1016/j.coi.2010.09.007
Fehrmann, 2011, Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA, PLoS Genet., 7, 10.1371/journal.pgen.1002197
Fairfax, 2012, Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles, Nat. Genet., 44, 502, 10.1038/ng.2205
Vandiedonck, 2011, Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex, Genome Res., 21, 1042, 10.1101/gr.116681.110
Lam, 2017, Unique allelic eQTL clusters in human MHC haplotypes, G3 (Bethesda), 7, 2595, 10.1534/g3.117.043828
Schwiebert, 1997, HLA-DRA promoter polymorphism and diversity generation within the immune system, Hum. Genet., 99, 801, 10.1007/s004390050452
Fernandez, 2003, Relative quantification of HLA-DRA1 and -DQA1 expression by real-time reverse transcriptase-polymerase chain reaction (RT-PCR), Eur. J. Immunogenet., 30, 141, 10.1046/j.1365-2370.2003.00376.x
Maffei, 1997, Polymorphism in the 5' terminal region of the mRNA of HLA-DQA1 gene: identification of four groups of transcripts and their association with polymorphism in the alpha 1 domain, Hum. Immunol., 53, 167, 10.1016/S0198-8859(97)83121-7
Del Pozzo, 1992, DNA polymorphisms in the 5'-flanking region of the HLA-DQA1 gene, Immunogenetics, 35, 176, 10.1007/BF00185111
Britten, 2009, Differential expression of HLA-DQ alleles in peripheral blood mononuclear cells: alleles associated with susceptibility to and protection from autoimmune type 1 diabetes, Int. J. Immunogenet., 36, 47, 10.1111/j.1744-313X.2008.00823.x
Morzycka-Wroblewska, 1993, Structure and evolution of the promoter regions of the DQA genes, Immunogenetics, 37, 364, 10.1007/BF00216801
Donner, 2002, Unbalanced amounts of HLA-DQA1 allele mRNA: DQA1*03 shows high and DQA1*0501 low amounts of mRNA in heterozygous individuals, Eur. J. Immunogenet., 29, 321, 10.1046/j.1365-2370.2002.00321.x
Beaty, 1995, Functional effects of a natural polymorphism in the transcriptional regulatory sequence of HLA-DQB1, Mol. Cell Biol., 15, 4771, 10.1128/MCB.15.9.4771
Vincent, 1996, Quantitative analysis of the expression of the HLA-DRB genes at the transcriptional level by competitive polymerase chain reaction, J. Immunol., 156, 603, 10.4049/jimmunol.156.2.603
Leen, 1994, Structural and functional analysis of HLA-DR beta-promoter polymorphism and isomorphism, Hum. Immunol., 41, 112, 10.1016/0198-8859(94)90003-5
Singal, 1996, Polymorphism in both X and Y box motifs controls level of expression of HLA-DRB1 genes, Immunogenetics, 43, 50
Singal, 1993, Polymorphism in the upstream regulatory regions of HLA-DRB genes, Immunogenetics, 37, 143, 10.1007/BF00216839
Louis, 1993, Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution, Immunogenetics, 38, 21, 10.1007/BF00216386
Maffei, 1997, Differential expression of insulin-dependent diabetes mellitus-associated HLA-DQA1 alleles in vivo, Eur. J. Immunol., 27, 1549, 10.1002/eji.1830270634
Cepek, 2016, DNA methylation and mRNA expression of HLA-DQA1 alleles in type 1 diabetes mellitus, Immunology, 148, 150, 10.1111/imm.12593
Zajacova, 2015, Differences in promoter DNA methylation and mRNA expression of individual alleles of the HLA class II DQA1 gene, Immunol. Lett., 167, 147, 10.1016/j.imlet.2015.08.006
Cavalli, 2016, MHC class II super-enhancer increases surface expression of HLA-DR and HLA-DQ and affects cytokine production in autoimmune vitiligo, Proc. Natl. Acad. Sci. U S A, 113, 1363, 10.1073/pnas.1523482113
Vander Lugt, 2014, Transcriptional programming of dendritic cells for enhanced MHC class II antigen presentation, Nat. Immunol., 15, 161, 10.1038/ni.2795
Horton, 2008, Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project, Immunogenetics, 60, 1, 10.1007/s00251-007-0262-2
International, 2009, Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases, Proc. Natl. Acad. Sci. U S A, 106, 18680, 10.1073/pnas.0909307106
Vader, 2003, The HLA-DQ2 gene dose effect in celiac disease is directly related to the magnitude and breadth of gluten-specific T cell responses, Proc. Natl. Acad. Sci. U S A, 100, 12390, 10.1073/pnas.2135229100
Pisapia, 2016, HLA-DQ2.5 genes associated to celiac disease risk are preferentially expressed respect to non-predisposing HLA genes: implication for anti-gluten T cell response, J. Autoimmun., 70, 63, 10.1016/j.jaut.2016.03.016
Pisapia, 2013, Co-regulated expression of alpha and beta mRNAs encoding HLA-DR surface heterodimers is mediated by the MHCII RNA operon, Nucleic Acids Res., 41, 3772, 10.1093/nar/gkt059
Corso, 2011, EBP1 and DRBP76/NF90 binding proteins are included in the major histocompatibility complex class II RNA operon, Nucleic Acids Res., 39, 7263, 10.1093/nar/gkr278