{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T13:43:54Z","timestamp":1790775834211,"version":"4.1.0"},"posted":{"date-parts":[[2023,10,2]]},"group-title":"Immunology","reference-count":78,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Tissue-resident memory T (T\n                  <jats:sub>RM<\/jats:sub>\n                  ) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive T\n                  <jats:sub>RM<\/jats:sub>\n                  differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 T\n                  <jats:sub>RM<\/jats:sub>\n                  across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus T\n                  <jats:sub>RM<\/jats:sub>\n                  signature of 60 genes across skin and siIEL that can effectively distinguish T\n                  <jats:sub>RM<\/jats:sub>\n                  from circulating T cell populations, providing a more specific T\n                  <jats:sub>RM<\/jats:sub>\n                  signature than what was previously generated by comparing bulk T\n                  <jats:sub>RM<\/jats:sub>\n                  to na\u00efve or non-tissue resident memory populations. This updated T\n                  <jats:sub>RM<\/jats:sub>\n                  signature included the AP-1 transcription factor family members\n                  <jats:italic>Fos, Fosb<\/jats:italic>\n                  and\n                  <jats:italic>Fosl2<\/jats:italic>\n                  . Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature T\n                  <jats:sub>RM<\/jats:sub>\n                  .\n                  <jats:italic>CyCIF<\/jats:italic>\n                  tissue imaging detected nuclear co-localization of AP-1 members\n                  <jats:italic>Fosb<\/jats:italic>\n                  and\n                  <jats:italic>Junb<\/jats:italic>\n                  in resting CD8 T\n                  <jats:sub>RM<\/jats:sub>\n                  &gt;100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in T\n                  <jats:sub>RM<\/jats:sub>\n                  biology and suggests a novel mechanism for rapid reactivation of resting T\n                  <jats:sub>RM<\/jats:sub>\n                  in tissue upon antigen encounter.\n                <\/jats:p>","DOI":"10.1101\/2023.09.29.560006","type":"posted-content","created":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T00:32:43Z","timestamp":1696293163000},"source":"Crossref","is-referenced-by-count":9,"title":["Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1394-3158","authenticated-orcid":false,"given":"Neal P.","family":"Smith","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youdong","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason B.","family":"Williams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kasidet","family":"Manakongtreecheep","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shishir","family":"Pant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingxia","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tian","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"Stingley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander L.","family":"Kley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3364-1838","authenticated-orcid":false,"given":"Peter K.","family":"Sorger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra-Chlo\u00e9","family":"Villani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas S.","family":"Kupper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2023100903551599000_2023.09.29.560006v1.1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1442-9071.2011.02672.x"},{"key":"2023100903551599000_2023.09.29.560006v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/44385"},{"key":"2023100903551599000_2023.09.29.560006v1.3","doi-asserted-by":"crossref","unstructured":"Rotrosen, E. & Kupper, T. 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