{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:40:03Z","timestamp":1793320803318,"version":"4.5.0"},"reference-count":100,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T00:00:00Z","timestamp":1786147200000},"content-version":"am","delay-in-days":341,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["201908440236"],"award-info":[{"award-number":["201908440236"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002661","name":"FNRS","doi-asserted-by":"publisher","award":["PDR T.0230.18"],"award-info":[{"award-number":["PDR T.0230.18"]}],"id":[{"id":"10.13039\/501100002661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002661","name":"FNRS","doi-asserted-by":"publisher","award":["CDR J.0068.22"],"award-info":[{"award-number":["CDR J.0068.22"]}],"id":[{"id":"10.13039\/501100002661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010978","name":"Wallonie-Bruxelles International","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010978","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022690","name":"Breakthrough T1D","doi-asserted-by":"publisher","award":["3-SRA-2023-1379-S-B"],"award-info":[{"award-number":["3-SRA-2023-1379-S-B"]}],"id":[{"id":"10.13039\/100022690","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M and Harry B Helmsley Charitable Trust","doi-asserted-by":"publisher","award":["2402-08172"],"award-info":[{"award-number":["2402-08172"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Autoimmunity"],"published-print":{"date-parts":[[2025,9]]},"DOI":"10.1016\/j.jaut.2025.103469","type":"journal-article","created":{"date-parts":[[2025,8,8]],"date-time":"2025-08-08T04:19:28Z","timestamp":1754626768000},"page":"103469","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"special_numbering":"C","title":["Transcriptomics of autoimmune diseases identifies FGFR1 as a target for pancreatic \u03b2-cell protection"],"prefix":"10.1016","volume":"156","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6995-8573","authenticated-orcid":false,"given":"Xiaoyan","family":"Yi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Priscila L.","family":"Zimath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugenia","family":"Martin-Vazquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junior Garcia","family":"Oliveira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sayro","family":"Jawurek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra C.","family":"Title","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Burcak","family":"Yesildag","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nizar I.","family":"Mourad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antoine","family":"Buemi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7ois","family":"Pattou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Kerr-Conte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabine","family":"Costagliola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00edrian","family":"Romitti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Decio L.","family":"Eizirik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jaut.2025.103469_bib1","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.cell.2020.03.007","article-title":"Challenges, progress, and prospects of developing therapies to treat autoimmune diseases","volume":"181","author":"Fugger","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2025.103469_bib2","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature13835","article-title":"Genetic and epigenetic fine mapping of causal autoimmune disease variants","volume":"518","author":"Farh","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2025.103469_bib3","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/nrendo.2013.131","article-title":"Type 2 diabetes mellitus--an autoimmune disease?","volume":"9","author":"Velloso","year":"2013","journal-title":"Nat. Rev. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib4","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/s41577-019-0213-9","article-title":"Targeting innate immune mediators in type 1 and type 2 diabetes","volume":"19","author":"Donath","year":"2019","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.jaut.2025.103469_bib5","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/nature25158","article-title":"Microglia-derived ASC specks cross-seed amyloid-\u03b2 in Alzheimer's disease","volume":"552","author":"Venegas","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.jaut.2025.103469_bib6","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1016\/S0140-6736(20)32205-4","article-title":"Alzheimer's disease","volume":"397","author":"Scheltens","year":"2021","journal-title":"Lancet"},{"key":"10.1016\/j.jaut.2025.103469_bib7","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abd7600","article-title":"Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis","volume":"7","author":"Szymczak","year":"2021","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jaut.2025.103469_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.molmet.2022.101565","article-title":"Beta cell and immune cell interactions in autoimmune type 1 diabetes: how they meet and talk to each other","volume":"64","author":"Scherm","year":"2022","journal-title":"Mol Metab"},{"key":"10.1016\/j.jaut.2025.103469_bib9","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1089\/ars.2017.7382","article-title":"Oxidative modifications in tissue pathology and autoimmune disease","volume":"29","author":"Yang","year":"2018","journal-title":"Antioxid Redox Signal"},{"key":"10.1016\/j.jaut.2025.103469_bib10","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1074\/jbc.272.3.1929","article-title":"Expression of neuronal traits in pancreatic beta cells. Implication of neuron-restrictive silencing factor\/repressor element silencing transcription factor, a neuron-restrictive silencer","volume":"272","author":"Atouf","year":"1997","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jaut.2025.103469_bib11","doi-asserted-by":"crossref","first-page":"3466","DOI":"10.1074\/jbc.M116.748335","article-title":"Neuron-enriched RNA-binding proteins regulate pancreatic beta cell function and survival","volume":"292","author":"Juan-Mateu","year":"2017","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.jaut.2025.103469_bib12","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1038\/s41591-022-01880-6","article-title":"The promise of precision medicine in rheumatology","volume":"28","author":"Guthridge","year":"2022","journal-title":"Nat Med"},{"key":"10.1016\/j.jaut.2025.103469_bib13","doi-asserted-by":"crossref","first-page":"322","DOI":"10.3389\/fimmu.2015.00322","article-title":"Antigen presentation, autoantigens, and immune regulation in multiple sclerosis and other autoimmune diseases","volume":"6","author":"Riedhammer","year":"2015","journal-title":"Front. Immunol."},{"key":"10.1016\/j.jaut.2025.103469_bib14","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1007\/s40265-017-0701-9","article-title":"JAK-STAT signaling as a target for inflammatory and autoimmune diseases: current and future prospects","volume":"77","author":"Banerjee","year":"2017","journal-title":"Drugs"},{"key":"10.1016\/j.jaut.2025.103469_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2022.105376","article-title":"Mining the transcriptome of target tissues of autoimmune and degenerative pancreatic \u03b2-cell and brain diseases to discover therapies","volume":"25","author":"Yi","year":"2022","journal-title":"iScience"},{"key":"10.1016\/j.jaut.2025.103469_bib16","doi-asserted-by":"crossref","first-page":"2140","DOI":"10.1056\/NEJMoa2306691","article-title":"Baricitinib and \u03b2-cell function in patients with new-onset type 1 diabetes","volume":"389","author":"Waibel","year":"2023","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.jaut.2025.103469_bib17","doi-asserted-by":"crossref","DOI":"10.3390\/jcm14051745","article-title":"The expanding therapeutic potential of deucravacitinib beyond psoriasis: a narrative review","volume":"14","author":"Bang","year":"2025","journal-title":"J. Clin. Med."},{"key":"10.1016\/j.jaut.2025.103469_bib18","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/nrendo.2016.30","article-title":"Viral infections in type 1 diabetes mellitus--why the \u03b2 cells?","volume":"12","author":"Op de Beeck","year":"2016","journal-title":"Nat. Rev. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib19","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/s41574-020-0355-7","article-title":"Pancreatic \u03b2-cells in type 1 and type 2 diabetes mellitus: different pathways to failure","volume":"16","author":"Eizirik","year":"2020","journal-title":"Nat. Rev. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib20","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1038\/s41588-019-0524-6","article-title":"The impact of proinflammatory cytokines on the \u03b2-cell regulatory landscape provides insights into the genetics of type 1 diabetes","volume":"51","author":"Ramos-Rodr\u00edguez","year":"2019","journal-title":"Nat. Genet."},{"key":"10.1016\/j.jaut.2025.103469_bib21","article-title":"Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets","volume":"5","author":"Patil","year":"2024","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.jaut.2025.103469_bib22","doi-asserted-by":"crossref","first-page":"2448","DOI":"10.1007\/s00125-016-4067-4","article-title":"Islet cell hyperexpression of HLA class I antigens: a defining feature in type 1 diabetes","volume":"59","author":"Richardson","year":"2016","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib23","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.ebiom.2018.09.040","article-title":"PDL1 is expressed in the islets of people with type 1 diabetes and is up-regulated by interferons-\u03b1 and-\u03b3 via IRF1 induction","volume":"36","author":"Colli","year":"2018","journal-title":"EBioMedicine"},{"key":"10.1016\/j.jaut.2025.103469_bib24","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/s11892-019-1245-z","article-title":"What the HLA-I!-Classical and non-classical HLA class I and their potential roles in type 1 diabetes","volume":"19","author":"Wyatt","year":"2019","journal-title":"Curr Diab Rep"},{"key":"10.1016\/j.jaut.2025.103469_bib25","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1016\/S0140-6736(15)60971-0","article-title":"Care of diabetes in children and adolescents: controversies, changes, and consensus","volume":"385","author":"Cameron","year":"2015","journal-title":"Lancet"},{"key":"10.1016\/j.jaut.2025.103469_bib26","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/S2213-8587(18)30112-8","article-title":"The challenge of modulating \u03b2-cell autoimmunity in type 1 diabetes","volume":"7","author":"Atkinson","year":"2019","journal-title":"Lancet Diabetes Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib27","doi-asserted-by":"crossref","first-page":"390","DOI":"10.2337\/dc20-0567","article-title":"Clinical impact of residual C-peptide secretion in type 1 diabetes on glycemia and microvascular complications","volume":"44","author":"Jeyam","year":"2021","journal-title":"Diabetes Care"},{"key":"10.1016\/j.jaut.2025.103469_bib28","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1016\/j.cmet.2020.04.005","article-title":"Patch-seq links single-cell transcriptomes to human islet dysfunction in diabetes","volume":"31","author":"Camunas-Soler","year":"2020","journal-title":"Cell Metab."},{"key":"10.1016\/j.jaut.2025.103469_bib29","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1007\/s00125-024-06106-7","article-title":"Interferons are key cytokines acting on pancreatic islets in type 1 diabetes","volume":"67","author":"Coomans de Brach\u00e8ne","year":"2024","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib30","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.2337\/dbi20-0046","article-title":"From pancreatic \u03b2-cell gene Networks to novel therapies for type 1 diabetes","volume":"70","author":"Eizirik","year":"2021","journal-title":"Diabetes"},{"key":"10.1016\/j.jaut.2025.103469_bib31","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","article-title":"A next generation connectivity Map: L1000 platform and the first 1,000,000 profiles","volume":"171","author":"Subramanian","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2025.103469_bib32","doi-asserted-by":"crossref","first-page":"988","DOI":"10.2337\/db18-0686","article-title":"HLA class II antigen processing and presentation pathway components demonstrated by transcriptome and protein analyses of islet \u03b2-cells from donors with type 1 diabetes","volume":"68","author":"Russell","year":"2019","journal-title":"Diabetes"},{"key":"10.1016\/j.jaut.2025.103469_bib33","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/s41467-022-28120-2","article-title":"Lymphocyte infiltration and thyrocyte destruction are driven by stromal and immune cell components in Hashimoto's thyroiditis","volume":"13","author":"Zhang","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib34","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108466","article-title":"Persistent or transient human \u03b2 cell dysfunction induced by metabolic stress: specific signatures and shared gene expression with type 2 diabetes","volume":"33","author":"Marselli","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.jaut.2025.103469_bib35","doi-asserted-by":"crossref","first-page":"13924","DOI":"10.1073\/pnas.1402665111","article-title":"Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism","volume":"111","author":"Fadista","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2025.103469_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2021.109807","article-title":"TIGER: the gene expression regulatory variation landscape of human pancreatic islets","volume":"37","author":"Alonso","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.jaut.2025.103469_bib37","doi-asserted-by":"crossref","first-page":"E302","DOI":"10.1073\/pnas.1716032115","article-title":"Cell-specific and region-specific transcriptomics in the multiple sclerosis model: focus on astrocytes","volume":"115","author":"Itoh","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jaut.2025.103469_bib38","doi-asserted-by":"crossref","first-page":"4490","DOI":"10.4049\/jimmunol.1601988","article-title":"CD40L-Dependent pathway is active at various stages of rheumatoid arthritis disease progression","volume":"198","author":"Guo","year":"2017","journal-title":"J. Immunol."},{"key":"10.1016\/j.jaut.2025.103469_bib39","doi-asserted-by":"crossref","first-page":"2364","DOI":"10.2337\/db20-0636","article-title":"A computational approach for defining a signature of \u03b2-cell golgi stress in diabetes","volume":"69","author":"Bone","year":"2020","journal-title":"Diabetes"},{"key":"10.1016\/j.jaut.2025.103469_bib40","doi-asserted-by":"crossref","first-page":"2584","DOI":"10.1038\/s41467-020-16327-0","article-title":"An integrated multi-omics approach identifies the landscape of interferon-\u03b1-mediated responses of human pancreatic beta cells","volume":"11","author":"Colli","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib41","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jaut.2025.103469_bib42","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jaut.2025.103469_bib43","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.jaut.2025.103469_bib44","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib45","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"GigaScience"},{"key":"10.1016\/j.jaut.2025.103469_bib46","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.jaut.2025.103469_bib47","doi-asserted-by":"crossref","first-page":"979","DOI":"10.12688\/f1000research.73600.1","article-title":"Doublet identification in single-cell sequencing data using scDblFinder","volume":"10","author":"Germain","year":"2021","journal-title":"F1000Res"},{"key":"10.1016\/j.jaut.2025.103469_bib48","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jaut.2025.103469_bib49","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s13059-021-02281-7","article-title":"scSorter: assigning cells to known cell types according to marker genes","volume":"22","author":"Guo","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.jaut.2025.103469_bib50","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.202302203","article-title":"RedRibbon: a new rank-rank hypergeometric overlap for gene and transcript expression signatures","volume":"7","author":"Piron","year":"2024","journal-title":"Life Sci. Alliance"},{"key":"10.1016\/j.jaut.2025.103469_bib51","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.jaut.2025.103469_bib52","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"10.1016\/j.jaut.2025.103469_bib53","doi-asserted-by":"crossref","first-page":"3589","DOI":"10.1172\/JCI58447","article-title":"A genetically engineered human pancreatic \u03b2 cell line exhibiting glucose-inducible insulin secretion","volume":"121","author":"Ravassard","year":"2011","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.jaut.2025.103469_bib54","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1007\/s00125-015-3669-6","article-title":"Cytokines induce endoplasmic reticulum stress in human, rat and mouse beta cells via different mechanisms","volume":"58","author":"Brozzi","year":"2015","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib55","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.regpep.2007.08.017","article-title":"An overview of pancreatic beta-cell defects in human type 2 diabetes: implications for treatment","volume":"146","author":"Marchetti","year":"2008","journal-title":"Regul. Pept."},{"key":"10.1016\/j.jaut.2025.103469_bib56","doi-asserted-by":"crossref","first-page":"6338","DOI":"10.1172\/JCI141455","article-title":"YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress","volume":"130","author":"De Franco","year":"2020","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.jaut.2025.103469_bib57","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2022.967765","article-title":"In depth functional characterization of human induced pluripotent stem cell-derived beta cells in vitro and in vivo","volume":"10","author":"Fantuzzi","year":"2022","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.jaut.2025.103469_bib58","doi-asserted-by":"crossref","first-page":"10302","DOI":"10.1093\/nar\/gky839","article-title":"Pancreatic \u03b2-cell tRNA hypomethylation and fragmentation link TRMT10A deficiency with diabetes","volume":"46","author":"Cosentino","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jaut.2025.103469_bib59","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.2337\/db08-1510","article-title":"PTPN2, a candidate gene for type 1 diabetes, modulates interferon-gamma-induced pancreatic beta-cell apoptosis","volume":"58","author":"Moore","year":"2009","journal-title":"Diabetes"},{"key":"10.1016\/j.jaut.2025.103469_bib60","doi-asserted-by":"crossref","first-page":"1968","DOI":"10.1172\/JCI117188","article-title":"Cytokines suppress human islet function irrespective of their effects on nitric oxide generation","volume":"93","author":"Eizirik","year":"1994","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.jaut.2025.103469_bib61","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1007\/s001250100021","article-title":"A choice of death--the signal-transduction of immune-mediated beta-cell apoptosis","volume":"44","author":"Eizirik","year":"2001","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib62","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1007\/s10549-013-2829-y","article-title":"Inhibition of FGFR signaling by PD173074 improves antitumor immunity and impairs breast cancer metastasis","volume":"143","author":"Ye","year":"2014","journal-title":"Breast Cancer Res. Treat."},{"key":"10.1016\/j.jaut.2025.103469_bib63","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abn5732","article-title":"Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic \u03b2 cells","volume":"8","author":"Szymczak","year":"2022","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jaut.2025.103469_bib64","first-page":"3390","article-title":"CTLs are targeted to kill beta cells in patients with type 1 diabetes through recognition of a glucose-regulated preproinsulin epitope","volume":"118","author":"Skowera","year":"2008","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.jaut.2025.103469_bib65","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1002\/stem.587","article-title":"A targeted NKX2.1 human embryonic stem cell reporter line enables identification of human basal forebrain derivatives","volume":"29","author":"Goulburn","year":"2011","journal-title":"Stem Cell."},{"key":"10.1016\/j.jaut.2025.103469_bib66","doi-asserted-by":"crossref","first-page":"7057","DOI":"10.1038\/s41467-022-34776-7","article-title":"Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism","volume":"13","author":"Romitti","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib67","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1006\/cyto.1998.0426","article-title":"Quantification of murine cytokine mRNAs using real time quantitative reverse transcriptase PCR","volume":"11","author":"Overbergh","year":"1999","journal-title":"Cytokine"},{"key":"10.1016\/j.jaut.2025.103469_bib68","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1080\/19382014.2021.1948282","article-title":"A functional genomic approach to identify reference genes for human pancreatic beta cell real-time quantitative RT-PCR analysis","volume":"13","author":"Alvelos","year":"2021","journal-title":"Islets"},{"key":"10.1016\/j.jaut.2025.103469_bib69","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1080\/14728222.2022.2029410","article-title":"GDF15: a potential therapeutic target for type 1 diabetes","volume":"26","author":"Sarkar","year":"2022","journal-title":"Expert Opin. Ther. Targets"},{"key":"10.1016\/j.jaut.2025.103469_bib70","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s11892-019-1194-6","article-title":"Alterations in beta cell identity in type 1 and type 2 diabetes","volume":"19","author":"Moin","year":"2019","journal-title":"Curr Diab Rep"},{"key":"10.1016\/j.jaut.2025.103469_bib71","doi-asserted-by":"crossref","first-page":"5896","DOI":"10.1093\/emboj\/17.20.5896","article-title":"Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain","volume":"17","author":"Mohammadi","year":"1998","journal-title":"Embo j"},{"key":"10.1016\/j.jaut.2025.103469_bib72","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.coi.2016.09.007","article-title":"A roadmap of the generation of neoantigens as targets of the immune system in type 1 diabetes","volume":"43","author":"Roep","year":"2016","journal-title":"Curr. Opin. Immunol."},{"key":"10.1016\/j.jaut.2025.103469_bib73","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1007\/s00125-020-05176-7","article-title":"Presumption of innocence for beta cells: why are they vulnerable autoimmune targets in type 1 diabetes?","volume":"63","author":"Mallone","year":"2020","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib74","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1038\/s41574-020-00409-6","article-title":"Revisiting the role of inflammation in the loss of pancreatic \u03b2-cells in T1DM","volume":"16","author":"Eizirik","year":"2020","journal-title":"Nat. Rev. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib75","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1111\/j.1365-2249.2009.04053.x","article-title":"Gene expression profiles for the human pancreas and purified islets in type 1 diabetes: new findings at clinical onset and in long-standing diabetes","volume":"159","author":"Planas","year":"2010","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.jaut.2025.103469_bib76","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1007\/s00125-021-05619-9","article-title":"Upregulation of HLA class II in pancreatic beta cells from organ donors with type 1 diabetes","volume":"65","author":"Quesada-Masachs","year":"2022","journal-title":"Diabetologia"},{"key":"10.1016\/j.jaut.2025.103469_bib77","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/S0140-6736(83)90629-3","article-title":"Role of aberrant HLA-DR expression and antigen presentation in induction of endocrine autoimmunity","volume":"2","author":"Bottazzo","year":"1983","journal-title":"Lancet"},{"key":"10.1016\/j.jaut.2025.103469_bib78","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.jaut.2011.01.002","article-title":"Analysis of the cumulative changes in Graves' disease thyroid glands points to IFN signature, plasmacytoid DCs and alternatively activated macrophages as chronicity determining factors","volume":"36","author":"Ruiz-Riol","year":"2011","journal-title":"J. Autoimmun."},{"issue":"11","key":"10.1016\/j.jaut.2025.103469_bib79","doi-asserted-by":"crossref","first-page":"2600","DOI":"10.1007\/s00125-024-06269-3","article-title":"Comment on the role of interferons in the pathology of beta cell destruction in type 1 diabetes. Reply to Lenzen S [letter]","volume":"67","author":"Eizirik","year":"2024","journal-title":"Diabetologia."},{"key":"10.1016\/j.jaut.2025.103469_bib80","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.abd6527","article-title":"Islet expression of type I interferon response sensors is associated with immune infiltration and viral infection in type 1 diabetes","volume":"7","author":"Apaolaza","year":"2021","journal-title":"Sci. Adv."},{"key":"10.1016\/j.jaut.2025.103469_bib81","doi-asserted-by":"crossref","first-page":"6363","DOI":"10.1038\/s41467-022-34069-z","article-title":"The type 1 diabetes gene TYK2 regulates \u03b2-cell development and its responses to interferon-\u03b1","volume":"13","author":"Chandra","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib82","doi-asserted-by":"crossref","first-page":"105734","DOI":"10.1016\/j.ebiom.2025.105734","article-title":"Evans-Molina C.Pharmacological inhibition of tyrosine protein-kinase 2 reduces islet inflammation and delays type 1 diabetes onset in mice","volume":"117","author":"Syed","year":"2025","journal-title":"EBioMedicine"},{"key":"10.1016\/j.jaut.2025.103469_bib83","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1038\/s41467-024-45573-9","article-title":"TYK2 signaling promotes the development of autoreactive CD8(+) cytotoxic T lymphocytes and type 1 diabetes","volume":"15","author":"Mine","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jaut.2025.103469_bib84","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/s41584-024-01153-1","article-title":"JAK inhibitor selectivity: new opportunities, better drugs?","volume":"20","author":"Virtanen","year":"2024","journal-title":"Nat. Rev. Rheumatol."},{"key":"10.1016\/j.jaut.2025.103469_bib85","doi-asserted-by":"crossref","DOI":"10.1038\/s41573-025-01164-x","article-title":"Computational drug repurposing: approaches, evaluation of in silico resources and case studies","author":"Tanoli","year":"2025","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.jaut.2025.103469_bib86","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/nrd2792","article-title":"The FGF family: biology, pathophysiology and therapy","volume":"8","author":"Beenken","year":"2009","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.jaut.2025.103469_bib87","doi-asserted-by":"crossref","DOI":"10.1016\/j.ctrv.2021.102170","article-title":"Targeting FGFR inhibition in cholangiocarcinoma","volume":"95","author":"Goyal","year":"2021","journal-title":"Cancer Treat Rev."},{"key":"10.1016\/j.jaut.2025.103469_bib88","doi-asserted-by":"crossref","DOI":"10.1016\/j.phrs.2019.104567","article-title":"The role of fibroblast growth factor receptor (FGFR) protein-tyrosine kinase inhibitors in the treatment of cancers including those of the urinary bladder","volume":"151","author":"Roskoski","year":"2020","journal-title":"Pharmacol. Res."},{"key":"10.1016\/j.jaut.2025.103469_bib89","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1111\/cns.14176","article-title":"FGF\/FGFR system in the central nervous system demyelinating disease: recent progress and implications for multiple sclerosis","volume":"29","author":"Zhang","year":"2023","journal-title":"CNS Neurosci. Ther."},{"key":"10.1016\/j.jaut.2025.103469_bib90","doi-asserted-by":"crossref","DOI":"10.3390\/cells10040884","article-title":"FGF\/FGFR pathways in multiple sclerosis and in its disease models","volume":"10","author":"Rajendran","year":"2021","journal-title":"Cells"},{"key":"10.1016\/j.jaut.2025.103469_bib91","doi-asserted-by":"crossref","first-page":"2989","DOI":"10.1111\/bph.16186","article-title":"The small molecule fibroblast growth factor receptor inhibitor infigratinib exerts anti-inflammatory effects and remyelination in a model of multiple sclerosis","volume":"180","author":"Rajendran","year":"2023","journal-title":"Br. J. Pharmacol."},{"key":"10.1016\/j.jaut.2025.103469_bib92","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1111\/bph.17341","article-title":"Anti-inflammatory and remyelinating effects of fexagratinib in experimental multiple sclerosis","volume":"182","author":"Gurski","year":"2025","journal-title":"Br. J. Pharmacol."},{"key":"10.1016\/j.jaut.2025.103469_bib93","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1002\/art.42674","article-title":"Role and therapeutic potential for targeting fibroblast growth factor 10\/FGFR1 in relapsed rheumatoid arthritis","volume":"76","author":"Meng","year":"2024","journal-title":"Arthritis Rheumatol."},{"key":"10.1016\/j.jaut.2025.103469_bib94","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1038\/s41574-020-00443-4","article-title":"Type 1 diabetes mellitus as a disease of the \u03b2-cell (do not blame the immune system?)","volume":"17","author":"Roep","year":"2021","journal-title":"Nat. Rev. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib95","doi-asserted-by":"crossref","first-page":"569","DOI":"10.3389\/fendo.2020.00569","article-title":"Role of the PD-1\/PD-L1 dyad in the maintenance of pancreatic immune tolerance for prevention of type 1 diabetes","volume":"11","author":"Falcone","year":"2020","journal-title":"Front. Endocrinol."},{"key":"10.1016\/j.jaut.2025.103469_bib96","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1016\/j.cmet.2017.01.005","article-title":"\u03b2 cells that resist immunological attack develop during progression of autoimmune diabetes in NOD mice","volume":"25","author":"Rui","year":"2017","journal-title":"Cell Metab."},{"key":"10.1016\/j.jaut.2025.103469_bib97","doi-asserted-by":"crossref","DOI":"10.1016\/j.jaut.2019.05.013","article-title":"Analysis of the PD-1\/PD-L1 axis in human autoimmune thyroid disease: insights into pathogenesis and clues to immunotherapy associated thyroid autoimmunity","volume":"103","author":"\u00c1lvarez-Sierra","year":"2019","journal-title":"J. Autoimmun."},{"key":"10.1016\/j.jaut.2025.103469_bib98","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.cytogfr.2005.01.007","article-title":"Mechanisms underlying differential responses to FGF signaling","volume":"16","author":"Dailey","year":"2005","journal-title":"Cytokine Growth Factor Rev."},{"key":"10.1016\/j.jaut.2025.103469_bib99","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1111\/dom.14104","article-title":"Preclinical evaluation of tyrosine kinase 2 inhibitors for human beta-cell protection in type 1 diabetes","volume":"22","author":"Coomans de Brach\u00e8ne","year":"2020","journal-title":"Diabetes Obes Metab"},{"key":"10.1016\/j.jaut.2025.103469_bib100","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1007\/s00125-017-4536-4","article-title":"IFN-\u03b1 induces a preferential long-lasting expression of MHC class I in human pancreatic beta cells","volume":"61","author":"Coomans de Brach\u00e8ne","year":"2018","journal-title":"Diabetologia"}],"container-title":["Journal of Autoimmunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841125001143?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896841125001143?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T14:29:27Z","timestamp":1772807367000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896841125001143"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9]]},"references-count":100,"alternative-id":["S0896841125001143"],"URL":"https:\/\/doi.org\/10.1016\/j.jaut.2025.103469","relation":{},"ISSN":["0896-8411"],"issn-type":[{"value":"0896-8411","type":"print"}],"subject":[],"published":{"date-parts":[[2025,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptomics of autoimmune diseases identifies FGFR1 as a target for pancreatic \u03b2-cell protection","name":"articletitle","label":"Article Title"},{"value":"Journal of Autoimmunity","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jaut.2025.103469","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"103469"}}