DNA methylation differences within INS, PTPN22 and IL2RA promoters in lymphocyte subsets in children with type 1 diabetes and controls

References

• Robertson CC, Rich SS. Genetics of type 1 diabetes. Curr Opin Genet Dev. 2018;50:1–8.
   PubMed Web of Science ®Google Scholar
• Barrett JC, Clayton D, Concannon P, et al. Genome-wide association study and meta-analysis finds over 40 loci affect risk of type 1 diabetes. Nat Genet. 2009;41(6):703–707.
   PubMed Web of Science ®Google Scholar
• Onengut-Gumuscu S, Chen W-M, Burren O, et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet. 2015;47(4):381–386.
   PubMed Web of Science ®Google Scholar
• Robertson CC, Inshaw JRJ, Onengut-Gumuscu S, et al. Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes. Nat Genet. 2021;53(7):962–971.
   PubMed Web of Science ®Google Scholar
• Ram R, Morahan G. Effects of type 1 diabetes risk alleles on immune cell gene expression. Genes. 2017;8(6):167.
   PubMed Web of Science ®Google Scholar
• Gaunt TR, Shihab HA, Hemani G, et al. Systematic identification of genetic influences on methylation across the human life course. Genome Biol. 2016;17(1):61.
   PubMedGoogle Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–492.
   PubMed Web of Science ®Google Scholar
• Hirai N, Watanabe M, Inoue N, et al. Association of IL6 gene methylation in peripheral blood cells with the development and prognosis of autoimmune thyroid diseases. Autoimmunity. 2019;52(7-8):251–255.
   PubMed Web of Science ®Google Scholar
• Guimarães JR, Coêlho MdC, de Oliveira NFP. Contribution of DNA methylation to the pathogenesis of Sjögren’s syndrome: a review. Autoimmunity. 2022;55(4):215–222.
   PubMed Web of Science ®Google Scholar
• Morita E, Watanabe M, Inoue N, et al. Methylation levels of the TNFA gene are different between graves’ and Hashimoto’s diseases and influenced by the TNFA polymorphism. Autoimmunity. 2018;51(3):118–125.
   PubMed Web of Science ®Google Scholar
• Carry PM, Vanderlinden LA, Johnson RK, et al. DNA methylation near the INS gene is associated with INS genetic variation (rs689) and type 1 diabetes in the diabetes autoimmunity study in the young. Pediatr Diabetes. 2020;21(4):597–605.
   PubMed Web of Science ®Google Scholar
• Ye J, Richardson TG, McArdle WL, et al. Identification of loci where DNA methylation potentially mediates genetic risk of type 1 diabetes. J Autoimmun. 2018;93:66–75.
   PubMed Web of Science ®Google Scholar
• Belot M-P, Fradin D, Mai N, et al. CpG methylation changes within the IL2RA promoter in type 1 diabetes of childhood onset. PLOS One. 2013;8(7):e68093.
   PubMed Web of Science ®Google Scholar
• Fradin D, Le Fur S, Mille C, et al. Association of the CpG methylation pattern of the proximal insulin gene promoter with type 1 diabetes. PLOS One. 2012;7(5):e36278.
   PubMed Web of Science ®Google Scholar
• Kindt ASD, Fuerst RW, Knoop J, et al. Allele-specific methylation of type 1 diabetes susceptibility genes. J Autoimmun. 2018;89:63–74.
   PubMed Web of Science ®Google Scholar
• Johnson RK, Vanderlinden LA, Dong F, et al. Longitudinal DNA methylation differences precede type 1 diabetes. Sci Rep. 2020;10(1):3721.
   PubMed Web of Science ®Google Scholar
• Rakyan VK, Beyan H, Down TA, et al. Identification of type 1 diabetes–associated DNA methylation variable positions that precede disease diagnosis. PLOS Genet. 2011;7(9):e1002300.
   PubMed Web of Science ®Google Scholar
• Reinius LE, Acevedo N, Joerink M, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLOS One. 2012;7(7):e41361.
   PubMed Web of Science ®Google Scholar
• American Diabetes Association. 2. Classification and diagnosis of diabetes: standards of medical care in diabetes—2021. Diabetes Care. 2020;44: S15–S33.
   Web of Science ®Google Scholar
• Siljander HTA, Simell S, Hekkala A, et al. Predictive characteristics of diabetes-associated autoantibodies among children with HLA-conferred disease susceptibility in the general population. Diabetes. 2009;58(12):2835–2842.
   PubMed Web of Science ®Google Scholar
• Ilonen J, Kiviniemi M, Lempainen J, et al. Genetic susceptibility to type 1 diabetes in childhood – estimation of HLA class II associated disease risk and class II effect in various phases of islet autoimmunity. Pediatr Diabetes. 2016;17 Suppl 22:8–16.
   PubMedGoogle Scholar
• Dejeux E, Audard V, Cavard C, et al. Rapid identification of promoter hypermethylation in hepatocellular carcinoma by pyrosequencing of etiologically homogeneous sample pools. J Mol Diagn. 2007;9(4):510–520.
   PubMed Web of Science ®Google Scholar
• Mouzaki K, Kotanidou EP, Fragou A, et al. Insulin gene promoter methylation status in greek children and adolescents with type 1 diabetes. Biomed Rep. 2020;13(4):31.
   PubMed Web of Science ®Google Scholar
• Yang BT, Dayeh TA, Kirkpatrick CL, et al. Insulin promoter DNA methylation correlates negatively with insulin gene expression and positively with HbA(1c) levels in human pancreatic islets. Diabetologia. 2011;54(2):360–367.
   PubMed Web of Science ®Google Scholar
• Kuroda A, Rauch TA, Todorov I, et al. Insulin gene expression is regulated by DNA methylation. PLOS One. 2009;4(9):e6953.
   PubMed Web of Science ®Google Scholar
• Husseiny MI, Kaye A, Zebadua E, et al. Tissue-specific methylation of human insulin gene and PCR assay for monitoring beta cell death. PLOS One. 2014;9(4):e94591.
   PubMed Web of Science ®Google Scholar
• Neiman D, Moss J, Hecht M, et al. Islet cells share promoter hypomethylation independently of expression, but exhibit cell-type–specific methylation in enhancers. Proc Natl Acad Sci U S A. 2017;114(51):13525–13530.
   PubMed Web of Science ®Google Scholar
• Barratt BJ, Payne F, Lowe CE, et al. Remapping the insulin gene/IDDM2 locus in type 1 diabetes. Diabetes. 2004;53(7):1884–1889.
   PubMed Web of Science ®Google Scholar
• Vafiadis P, Bennett ST, Todd JA, et al. Insulin expression in human thymus is modulated by INS VNTR alleles at the IDDM2 locus. Nat Genet. 1997;15(3):289–292.
   PubMed Web of Science ®Google Scholar
• Pugliese A, Zeller M, Fernandez A, Jr, et al. The insulin gene is transcribed in the human thymus and transcription levels correlate with allelic variation at the INS VNTR-lDDM2 susceptibility locus for type 1 diabetes. Nat Genet. 1997;15(3):293–297.
   PubMed Web of Science ®Google Scholar
• Field J, Fox A, Jordan MA, et al. Interleukin-2 receptor-α proximal promoter hypomethylation is associated with multiple sclerosis. Genes Immun. 2017;18(2):59–66.
   PubMed Web of Science ®Google Scholar
• Kyrgios I, Fragou A, Kotanidou EP, et al. DNA methylation analysis within the IL2RA gene promoter in youth with autoimmune thyroid disease. Eur J Clin Invest. 2020;50:e13199.
   PubMed Web of Science ®Google Scholar
• Belot M-P, Castell A-L, Le Fur S, et al. Dynamic demethylation of the IL2RA promoter during in vitro CD4+ T cell activation in association with IL2RA expression. Epigenetics. 2018;13(5):459–472.
   PubMed Web of Science ®Google Scholar
• Kyrgios I, Giza S, Fragou A, et al. DNA hypermethylation of PTPN22 gene promoter in children and adolescents with Hashimoto thyroiditis. J Endocrinol Invest. 2021;44(10):2131–2138.
   PubMed Web of Science ®Google Scholar
• Chandra A, Senapati S, Roy S, et al. Epigenome-wide DNA methylation regulates cardinal pathological features of psoriasis. Clin Epigenetics. 2018;10(1):108.
   PubMedGoogle Scholar
• Starskaia I, Laajala E, Grönroos T, et al. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia. 2022;65(5):844–860.
   PubMed Web of Science ®Google Scholar