{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:33:06Z","timestamp":1790843586399,"version":"4.1.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R01 AI124512"],"award-info":[{"award-number":["R01 AI124512"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["2T32AI007313"],"award-info":[{"award-number":["2T32AI007313"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Recent studies have demonstrated that regulatory T cells (Tregs) develop in the thymus via two pathways involving distinct Treg progenitors (TregP): CD25+FOXP3\u2212 (CD25+ TregP) and CD25\u2212FOXP3lo (FOXP3lo TregP) Treg progenitors. To examine this process in more detail, we carried out single-cell RNA sequencing (scRNA-Seq) and TCR-Seq on sorted murine CD4+CD8+ double-positive (DP) thymocytes, CD4+ single-positive (CD4SP) thymocytes, CD25+FOXP3\u2212CD73\u2212 TregP, CD25\u2212FOXP3loCD73\u2212 TregP, newly generated mature CD25+FOXP3+CD73\u2212 Tregs, and FOXP3+CD73+ recirculating\/long-term resident Tregs (RT-Tregs). Sorted populations were individually hashtagged and then combined into one scRNA-Seq\/TCR-Seq library before sequencing and subsequent analysis. We found that both CD25+ TregP and FOXP3lo TregP arise via an initial agonist-activated state that gives rise to a second transitional stage before differentiating into mature Tregs. Using both scRNA-Seq and bulk RNA-Seq on sorted thymocyte subsets, we demonstrate that CD25+ TregP are significantly enriched for Il2 production, suggesting that they are the major source of IL-2 needed to convert TregP into mature Tregs. Using TCR-Seq, we found that several TCRs were clearly biased in favor of the conventional or Treg lineages, but that a large fraction of TCRs were found in both these lineages. Finally, we found that RT-Tregs in the thymus are not monomorphic but are composed of multiple distinct subsets and that these RT-Tregs express the most diverse TCR repertoire of all CD4SP thymocytes. Thus, our studies define multiple stages of Treg differentiation within the murine thymus and serve as a resource for future studies on CD4+ thymocyte development and Treg differentiation.<\/jats:p>","DOI":"10.4049\/jimmunol.2200089","type":"journal-article","created":{"date-parts":[[2022,10,20]],"date-time":"2022-10-20T17:48:16Z","timestamp":1666288096000},"page":"1300-1313","source":"Crossref","is-referenced-by-count":19,"title":["Tracking Regulatory T Cell Development in the Thymus Using Single-Cell RNA Sequencing\/TCR Sequencing"],"prefix":"10.1093","volume":"209","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1099-0605","authenticated-orcid":false,"given":"David L","family":"Owen","sequence":"first","affiliation":[{"name":"Center for Immunology, University of Minnesota , Minneapolis, MN"},{"name":"Masonic Cancer Center, University of Minnesota , Minneapolis, MN"},{"name":"Department of Laboratory Medicine and Pathology, University of Minnesota , Minneapolis, MN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca S","family":"La Rue","sequence":"additional","affiliation":[{"name":"Minnesota Supercomputing Institute, University of Minnesota , Minneapolis, MN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah A","family":"Munro","sequence":"additional","affiliation":[{"name":"Minnesota Supercomputing Institute, University of Minnesota , Minneapolis, MN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5569-0366","authenticated-orcid":false,"given":"Michael A","family":"Farrar","sequence":"additional","affiliation":[{"name":"Center for Immunology, University of Minnesota , Minneapolis, MN"},{"name":"Masonic Cancer Center, University of Minnesota , Minneapolis, MN"},{"name":"Department of Laboratory Medicine and Pathology, University of Minnesota , Minneapolis, MN"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,1]]},"reference":[{"key":"2025021008330232000_r1","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.4049\/jimmunol.1900662","article-title":"Regulatory T cell development in the thymus","volume":"203","author":"Owen","year":"2019","journal-title":"J. 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