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However, it remains unclear how Aire deficiency influences immune cell development and function. Recent studies show that Aire-expressing thymic epithelial cells produce type I and III interferons, but how impaired IFN signalling from Aire deficiency contributes to immune dysregulation remains unclear. Single-cell RNA sequencing was used to profile immune cells from Aire-deficient and wild-type mice across thymus, bone marrow, and lymph nodes. In the thymus, thymocytes at late maturation stages, non-conventional T cells, myeloid cells, immature Ccl21+ mTECs and cTECs had reduced expression of type I interferon-stimulated genes in the absence of Aire. In contrast, interferon-stimulated gene expression in bone marrow immune cells appeared independent of Aire. These findings support a role for Aire in thymic interferon production and highlight type I IFNs\u2019 influence on transcriptomes of developing immune cells.<\/jats:p>","DOI":"10.1038\/s42003-025-09317-9","type":"journal-article","created":{"date-parts":[[2025,12,9]],"date-time":"2025-12-09T09:26:46Z","timestamp":1765272406000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Aire-dependent interferon signalling shapes thymocyte maturation and central tolerance in mice"],"prefix":"10.1038","volume":"9","author":[{"given":"Adrianna","family":"Jebrzycka","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2889-7342","authenticated-orcid":false,"given":"Lars","family":"Breivik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Dolan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yael","family":"Goldfarb","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1745-8996","authenticated-orcid":false,"given":"Jakub","family":"Abramson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8485-2248","authenticated-orcid":false,"given":"Anette S. 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