{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:19:12Z","timestamp":1785406752877,"version":"3.56.0"},"posted":{"date-parts":[[2026,2,26]]},"group-title":"Immunology","reference-count":74,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T00:00:00Z","timestamp":1772064000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R00CA234430"],"award-info":[{"award-number":["R00CA234430"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01A1177864"],"award-info":[{"award-number":["R01A1177864"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R21AI171745"],"award-info":[{"award-number":["R21AI171745"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R21AG084251"],"award-info":[{"award-number":["R21AG084251"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["5T32GM135123- 02"],"award-info":[{"award-number":["5T32GM135123- 02"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["T32CA196589"],"award-info":[{"award-number":["T32CA196589"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/00kbbk236","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/05snapr15","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/02j4jwp55","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/03ayy2w09","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/043ehm030","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/04q9fhm49","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,2,27]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                <jats:p>\n                  Immune responses evolve across time and tissues through coordinated programs of proliferation, differentiation, and migration, yet most single-cell measurements capture only static molecular snapshots. As a result, reconstructing how immune cells transition between alternative fates remains challenging, particularly for CD8 T cells, whose differentiation is highly dynamic and shaped by rapid expansion, contraction, and tissue trafficking. Here, we introduce an optimal transport-based fate mapping framework that reconstructs continuous CD8 T cell trajectories across time and tissues. Applied to longitudinal single-cell RNA-seq data from CD8 T cells responding to acute viral infection in mice, this approach accurately recapitulates population dynamics and resolves coherent effector and memory T cell differentiation trajectories. Extending the model to multiple tissues, we identify and experimentally validate temporally distinct waves of migration into the small intestine that give rise to divergent tissue-resident memory (T\n                  <jats:sc>rm<\/jats:sc>\n                  ) fates, long-lived T cells crucial in immunosurveillance. By integrating optimal transport inference with time-resolved\n                  <jats:italic>in vivo<\/jats:italic>\n                  labeling, we demonstrate that CD52 marks recent tissue entrants and distinguishes them from T\n                  <jats:sc>rm<\/jats:sc>\n                  precursors. Finally, trajectory-guided analysis of transcription factor regulons reveals both shared and context-specific gene regulatory programs and identifies AP4 as a key regulator of circulating versus tissue-resident specification. These results establish optimal transport as a principled framework for reconstructing immune cell fate dynamics and provide a quantitative map of early events governing antiviral CD8 T cell differentiation across tissues.\n                <\/jats:p>","DOI":"10.64898\/2026.02.24.707057","type":"posted-content","created":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:15:11Z","timestamp":1772154911000},"source":"Crossref","is-referenced-by-count":0,"title":["Optimal transport fate mapping resolves T cell differentiation dynamics across tissues"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3831-9845","authenticated-orcid":false,"given":"Alec L.","family":"Plotkin","sequence":"first","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1646-5710","authenticated-orcid":false,"given":"Genevieve N.","family":"Mullins","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William D.","family":"Green","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huitong","family":"Shi","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7028-2432","authenticated-orcid":false,"given":"H. Kay","family":"Chung","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8686-1638","authenticated-orcid":false,"given":"Natalie","family":"Stanley","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0752-2130","authenticated-orcid":false,"given":"J. Justin","family":"Milner","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"},{"name":"Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026030301500676000_2026.02.24.707057v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3031"},{"key":"2026030301500676000_2026.02.24.707057v2.2","doi-asserted-by":"publisher","DOI":"10.1038\/s12276-023-01105-x"},{"key":"2026030301500676000_2026.02.24.707057v2.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-020-0307-4"},{"key":"2026030301500676000_2026.02.24.707057v2.4","doi-asserted-by":"publisher","DOI":"10.1038\/nri3442"},{"key":"2026030301500676000_2026.02.24.707057v2.5","doi-asserted-by":"publisher","DOI":"10.48550\/arxiv.2102.09204"},{"key":"2026030301500676000_2026.02.24.707057v2.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.02.021"},{"key":"2026030301500676000_2026.02.24.707057v2.7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0015423"},{"key":"2026030301500676000_2026.02.24.707057v2.8","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-025-02877-y"},{"key":"2026030301500676000_2026.02.24.707057v2.9","doi-asserted-by":"publisher","DOI":"10.1101\/gr.279126.124"},{"key":"2026030301500676000_2026.02.24.707057v2.10","doi-asserted-by":"publisher","DOI":"10.1136\/jitc-2025-011761"},{"key":"2026030301500676000_2026.02.24.707057v2.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2025.04.030"},{"key":"2026030301500676000_2026.02.24.707057v2.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2020.04.007"},{"key":"2026030301500676000_2026.02.24.707057v2.13","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aaz6894"},{"key":"2026030301500676000_2026.02.24.707057v2.14","doi-asserted-by":"publisher","DOI":"10.1101\/2023.01.03.522354"},{"key":"2026030301500676000_2026.02.24.707057v2.15","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-023-02371-y"},{"key":"2026030301500676000_2026.02.24.707057v2.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2024.06.014"},{"key":"2026030301500676000_2026.02.24.707057v2.17","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4772-0"},{"key":"2026030301500676000_2026.02.24.707057v2.18","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3971"},{"key":"2026030301500676000_2026.02.24.707057v2.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-0591-3"},{"key":"2026030301500676000_2026.02.24.707057v2.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2022.09.011"},{"key":"2026030301500676000_2026.02.24.707057v2.21","doi-asserted-by":"publisher","DOI":"10.1038\/nature25144"},{"key":"2026030301500676000_2026.02.24.707057v2.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2018.03.015"},{"key":"2026030301500676000_2026.02.24.707057v2.23","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20090858"},{"key":"2026030301500676000_2026.02.24.707057v2.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.01.006"},{"key":"2026030301500676000_2026.02.24.707057v2.25","doi-asserted-by":"publisher","DOI":"10.48550\/arxiv.2106.06345"},{"key":"2026030301500676000_2026.02.24.707057v2.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08453-2"},{"key":"2026030301500676000_2026.02.24.707057v2.27","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1010492"},{"key":"2026030301500676000_2026.02.24.707057v2.28","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08466-x"},{"key":"2026030301500676000_2026.02.24.707057v2.29","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01556-22"},{"key":"2026030301500676000_2026.02.24.707057v2.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2011.07.010"},{"key":"2026030301500676000_2026.02.24.707057v2.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-022-01338-4"},{"key":"2026030301500676000_2026.02.24.707057v2.32","doi-asserted-by":"publisher","DOI":"10.1038\/nri3307"},{"key":"2026030301500676000_2026.02.24.707057v2.33","doi-asserted-by":"publisher","DOI":"10.1126\/science.1235487"},{"key":"2026030301500676000_2026.02.24.707057v2.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109174"},{"key":"2026030301500676000_2026.02.24.707057v2.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2024.01.004"},{"key":"2026030301500676000_2026.02.24.707057v2.36","doi-asserted-by":"publisher","DOI":"10.1016\/j.vaccine.2014.10.007"},{"key":"2026030301500676000_2026.02.24.707057v2.37","doi-asserted-by":"publisher","DOI":"10.1038\/s41590-022-01337-5"},{"key":"2026030301500676000_2026.02.24.707057v2.38","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3001983"},{"key":"2026030301500676000_2026.02.24.707057v2.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-04248-x"},{"key":"2026030301500676000_2026.02.24.707057v2.40","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-021-00329-9"},{"key":"2026030301500676000_2026.02.24.707057v2.41","doi-asserted-by":"publisher","DOI":"10.48550\/arxiv.2306.09099"},{"key":"2026030301500676000_2026.02.24.707057v2.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2007.08.007"},{"key":"2026030301500676000_2026.02.24.707057v2.43","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2023.12.006"},{"key":"2026030301500676000_2026.02.24.707057v2.44","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.179.5.2944"},{"key":"2026030301500676000_2026.02.24.707057v2.45","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.75.22.10663-10669.2001"},{"key":"2026030301500676000_2026.02.24.707057v2.46","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1101443"},{"key":"2026030301500676000_2026.02.24.707057v2.47","year":"2020","journal-title":"UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction"},{"key":"2026030301500676000_2026.02.24.707057v2.48","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.8.4911-4927.2003"},{"key":"2026030301500676000_2026.02.24.707057v2.49","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20202512"},{"key":"2026030301500676000_2026.02.24.707057v2.50","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2008571117"},{"key":"2026030301500676000_2026.02.24.707057v2.51","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1901512"},{"key":"2026030301500676000_2026.02.24.707057v2.52","doi-asserted-by":"publisher","DOI":"10.1126\/science.adn2337"},{"key":"2026030301500676000_2026.02.24.707057v2.53","doi-asserted-by":"publisher","DOI":"10.1038\/nature04882"},{"key":"2026030301500676000_2026.02.24.707057v2.54","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-042617-053214"},{"key":"2026030301500676000_2026.02.24.707057v2.55","doi-asserted-by":"publisher","DOI":"10.1038\/nature24993"},{"key":"2026030301500676000_2026.02.24.707057v2.56","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad2035"},{"key":"2026030301500676000_2026.02.24.707057v2.57","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.2400268"},{"key":"2026030301500676000_2026.02.24.707057v2.58","doi-asserted-by":"publisher","DOI":"10.1038\/ni.2744"},{"key":"2026030301500676000_2026.02.24.707057v2.59","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2014.03.007"},{"key":"2026030301500676000_2026.02.24.707057v2.60","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.4049\/jimmunol.155.4.1873","article-title":"Ly-6C is a marker of memory CD8+ T cells","volume":"155","year":"1995","journal-title":"J. Immunol"},{"key":"2026030301500676000_2026.02.24.707057v2.61","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201040760"},{"key":"2026030301500676000_2026.02.24.707057v2.62","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463"},{"key":"2026030301500676000_2026.02.24.707057v2.63","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0336-2"},{"key":"2026030301500676000_2026.02.24.707057v2.64","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2015.11.008"},{"key":"2026030301500676000_2026.02.24.707057v2.65","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3706"},{"key":"2026030301500676000_2026.02.24.707057v2.66","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2014.09.007"},{"key":"2026030301500676000_2026.02.24.707057v2.67","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2016.07.023"},{"key":"2026030301500676000_2026.02.24.707057v2.68","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.768541"},{"key":"2026030301500676000_2026.02.24.707057v2.69","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0"},{"key":"2026030301500676000_2026.02.24.707057v2.70","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188746"},{"key":"2026030301500676000_2026.02.24.707057v2.71","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3192"},{"key":"2026030301500676000_2026.02.24.707057v2.72","doi-asserted-by":"publisher","DOI":"10.1561\/2200000073"},{"key":"2026030301500676000_2026.02.24.707057v2.73","unstructured":"Cuturi, M. (2013). Sinkhorn Distances: Lightspeed Computation of Optimal Transport. In Advances in Neural Information Processing Systems (Curran Associates, Inc.)."},{"key":"2026030301500676000_2026.02.24.707057v2.74","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad547"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.02.24.707057","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T09:52:34Z","timestamp":1772531554000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.02.24.707057"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,26]]},"references-count":74,"URL":"https:\/\/doi.org\/10.64898\/2026.02.24.707057","relation":{},"subject":[],"published":{"date-parts":[[2026,2,26]]},"subtype":"preprint"}}