Eizirik DL, Pasquali L, Cnop M (2020) Pancreatic beta-cells in type 1 and type 2 diabetes mellitus: different pathways to failure. Nat Rev Endocrinol 16(7):349–362. https://doi.org/10.1038/s41574-020-0355-7

Article  CAS  PubMed  Google Scholar 

Atkinson MA, Eisenbarth GS, Michels AW (2014) Type 1 diabetes. Lancet 383(9911):69–82. https://doi.org/10.1016/S0140-6736(13)60591-7

Article  PubMed  Google Scholar 

Mathieu C, Martens PJ, Vangoitsenhoven R (2021) One hundred years of insulin therapy. Nat Rev Endocrinol 17(12):715–725. https://doi.org/10.1038/s41574-021-00542-w

Article  PubMed  Google Scholar 

Ramos-Rodriguez M, Raurell-Vila H, Colli ML et al (2019) The impact of proinflammatory cytokines on the beta-cell regulatory landscape provides insights into the genetics of type 1 diabetes. Nat Genet 51(11):1588–1595. https://doi.org/10.1038/s41588-019-0524-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Calderon B, Suri A, Pan XO, Mills JC, Unanue ER (2008) IFN-gamma-dependent regulatory circuits in immune inflammation highlighted in diabetes. J Immunol 181(10):6964–6974. https://doi.org/10.4049/jimmunol.181.10.6964

Article  CAS  PubMed  Google Scholar 

Colli ML, Ramos-Rodriguez M, Nakayasu ES et al (2020) An integrated multi-omics approach identifies the landscape of interferon-alpha-mediated responses of human pancreatic beta cells. Nat Commun 11(1):2584. https://doi.org/10.1038/s41467-020-16327-0

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Roca-Rivada A, Marin-Canas S, Colli ML et al (2023) Inhibition of the type 1 diabetes candidate gene PTPN2 aggravates TNF-alpha-induced human beta cell dysfunction and death. Diabetologia 66(8):1544–1556. https://doi.org/10.1007/s00125-023-05908-5

Article  CAS  PubMed  Google Scholar 

Ferreira RC, Guo H, Coulson RM et al (2014) A type I interferon transcriptional signature precedes autoimmunity in children genetically at risk for type 1 diabetes. Diabetes 63(7):2538–2550. https://doi.org/10.2337/db13-1777

Article  PubMed  PubMed Central  Google Scholar 

Marroqui L, Dos Santos RS, Op de Beeck A et al (2017) Interferon-alpha mediates human beta cell HLA class I overexpression, endoplasmic reticulum stress and apoptosis, three hallmarks of early human type 1 diabetes. Diabetologia 60(4):656–667. https://doi.org/10.1007/s00125-016-4201-3

Article  CAS  PubMed  Google Scholar 

Richardson SJ, Pugliese A (2021) 100 years of insulin: Pancreas pathology in type 1 diabetes: an evolving story. J Endocrinol 252(2):R41–r57. https://doi.org/10.1530/joe-21-0358

Article  CAS  PubMed  Google Scholar 

Hu X, Li J, Fu M, Zhao X, Wang W (2021) The JAK/STAT signaling pathway: from bench to clinic. Signal Transduct Target Ther 6(1):402. https://doi.org/10.1038/s41392-021-00791-1

Article  PubMed  PubMed Central  Google Scholar 

Eizirik DL, Szymczak F, Alvelos MI, Martin F (2021) From pancreatic beta-cell gene networks to novel therapies for type 1 diabetes. Diabetes 70(9):1915–1925. https://doi.org/10.2337/dbi20-0046

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stark GR, Kerr IM, Williams BR, Silverman RH, Schreiber RD (1998) How cells respond to interferons. Annu Rev Biochem 67:227–264. https://doi.org/10.1146/annurev.biochem.67.1.227

Article  CAS  PubMed  Google Scholar 

Tau G, Rothman P (1999) Biologic functions of the IFN-gamma receptors. Allergy 54(12):1233–1251. https://doi.org/10.1034/j.1398-9995.1999.00099.x

Article  CAS  PubMed  Google Scholar 

Achenbach P, Hippich M, Zapardiel-Gonzalo J et al (2022) A classification and regression tree analysis identifies subgroups of childhood type 1 diabetes. EBioMedicine 82:104118. https://doi.org/10.1016/j.ebiom.2022.104118

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nicoletti F, Zaccone P, Di Marco R et al (1996) The effects of a nonimmunogenic form of murine soluble interferon-gamma receptor on the development of autoimmune diabetes in the NOD mouse. Endocrinology 137(12):5567–5575. https://doi.org/10.1210/endo.137.12.8940385

Article  CAS  PubMed  Google Scholar 

Debray-Sachs M, Carnaud C, Boitard C et al (1991) Prevention of diabetes in NOD mice treated with antibody to murine IFN gamma. J Autoimmun 4(2):237–248. https://doi.org/10.1016/0896-8411(91)90021-4

Article  CAS  PubMed  Google Scholar 

De George DJ, Ge T, Krishnamurthy B, Kay TWH, Thomas HE (2023) Inflammation versus regulation: how interferon-gamma contributes to type 1 diabetes pathogenesis. Front Cell Dev Biol 11:1205590. https://doi.org/10.3389/fcell.2023.1205590

Article  PubMed  PubMed Central  Google Scholar 

Cnop M, Welsh N, Jonas JC, Jorns A, Lenzen S, Eizirik DL (2005) Mechanisms of pancreatic beta-cell death in type 1 and type 2 diabetes: many differences, few similarities. Diabetes 54(Suppl 2):S97–S107. https://doi.org/10.2337/diabetes.54.suppl_2.s97

Article  CAS  PubMed  Google Scholar 

Brozzi F, Nardelli TR, Lopes M et al (2015) Cytokines induce endoplasmic reticulum stress in human, rat and mouse beta cells via different mechanisms. Diabetologia 58(10):2307–2316. https://doi.org/10.1007/s00125-015-3669-6

Article  CAS  PubMed  Google Scholar 

Szymczak F, Colli ML, Mamula MJ, Evans-Molina C, Eizirik DL (2021) Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. Sci Adv 7(2). https://doi.org/10.1126/sciadv.abd7600

Ravassard P, Hazhouz Y, Pechberty S et al (2011) A genetically engineered human pancreatic beta cell line exhibiting glucose-inducible insulin secretion. J Clin Invest 121(9):3589–3597. https://doi.org/10.1172/JCI58447

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nacher M, Estil LE, Garcia A et al (2016) Human serum versus human serum albumin supplementation in human islet pretransplantation culture: in vitro and in vivo assessment. Cell Transplant 25(2):343–352. https://doi.org/10.3727/096368915X688119

Article  PubMed  Google Scholar 

Marchetti P, Dotta F, Lauro D, Purrello F (2008) An overview of pancreatic beta-cell defects in human type 2 diabetes: implications for treatment. Regul Pept 146(1-3):4–11. https://doi.org/10.1016/j.regpep.2007.08.017

Article  CAS  PubMed  Google Scholar 

Gennady K, Vladimir S, Nikolay B, Boris S, Maxim NA, Alexey S (2021) Fast gene set enrichment analysis. bioRxiv:060012. https://doi.org/10.1101/060012

Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30. https://doi.org/10.1093/nar/28.1.27

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fabregat A, Jupe S, Matthews L et al (2018) The reactome pathway knowledgebase. Nucleic Acids Res 46(D1):D649–D655. https://doi.org/10.1093/nar/gkx1132

Article  CAS  PubMed  Google Scholar 

Plaisier SB, Taschereau R, Wong JA, Graeber TG (2010) Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res 38(17):e169. https://doi.org/10.1093/nar/gkq636

Article  CAS  PubMed  PubMed Central  Google Scholar 

Piron A, Szymczak F, Papadopoulou T et al (2024) RedRibbon: A new rank-rank hypergeometric overlap for gene and transcript expression signatures. Life Sci Alliance 7(2). https://doi.org/10.26508/lsa.202302203

Russell MA, Redick SD, Blodgett DM et al (2019) HLA class II antigen processing and presentation pathway components demonstrated by transcriptome and protein analyses of islet beta-cells from donors with type 1 diabetes. Diabetes 68(5):988–1001. https://doi.org/10.2337/db18-0686

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moore F, Colli ML, Cnop M et al (2009) PTPN2, a candidate gene for type 1 diabetes, modulates interferon-gamma-induced pancreatic beta-cell apoptosis. Diabetes 58(6):1283–1291. https://doi.org/10.2337/db08-1510

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoorens A, Van de Casteele M, Kloppel G, Pipeleers D (1996) Glucose promotes survival of rat pancreatic beta cells by activating synthesis of proteins which suppress a constitutive apoptotic program. J Clin Invest 98(7):1568–1574. https://doi.org/10.1172/JCI118950

Article  CAS  PubMed  PubMed Central  Google Scholar 

Szymczak F, Alvelos MI, Marin-Canas S et al (2022) Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic beta cells. Sci Adv 8(37):eabn5732. https://doi.org/10.1126/sciadv.abn5732

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vitting-Seerup K, Sandelin A (2019) IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences. Bioinformatics 35(21):4469–4471. https://doi.org/10.1093/bioinformatics/btz247

Article  CAS  PubMed