{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:43Z","timestamp":1792790383427,"version":"4.5.0"},"posted":{"date-parts":[[2026,4,22]]},"group-title":"Genomics","reference-count":68,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:00:00Z","timestamp":1776816000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"IGVF","award":["HG011986"],"award-info":[{"award-number":["HG011986"]}]},{"name":"IGVF","award":["HG012053"],"award-info":[{"award-number":["HG012053"]}]},{"name":"NIH","award":["R01CA289574"],"award-info":[{"award-number":["R01CA289574"]}]},{"name":"NIH","award":["RM1HG011123"],"award-info":[{"award-number":["RM1HG011123"]}]},{"name":"Duke-Coulter Translational Partnership"},{"name":"Yosemite Management, LLC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,4,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Transcription factors (TFs) collaborate to regulate gene expression programs that define cell fate. In CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cells, this coordinated regulation underlies exhaustion, a dysfunctional state that constrains immunity in chronic infection and cancer. Here, we screen for cell state-specific TFs by performing pooled overexpression screens of 3,548 TF and TF isoforms in primary T cells across multiple CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cell states. We identify 82 regulators that collaborate with exhaustion-specific programs and profile their effects using perturb-SHARE-seq, connecting perturbations to changes in chromatin accessibility and gene expression across 702,314 single cells. We identify 38 reproducible regulatory programs and construct a map of 12,616 TF-program connections that shape CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cell states, nominating KLF2 as predictive of positive response to CAR-T therapy. Using seq2PRINT, a deep learning framework that predicts functional TF interactions, we identify RUNX as a \u201cmaster collaborator\u201d, a TF that broadly collaborates with other factors, and uncover a RUNX2:KLF2 interaction that specifies exhaustion-associated programs. Mutation of the RUNX2:KLF2 protein interface attenuates KLF2-mediated repression of exhaustion, while synthetic tethering of RUNX2 to KLF2 leads to an amplification of the phenotype. More broadly, we identify the collaborative action of RUNX as a driver in CD8\n                  <jats:sup>+<\/jats:sup>\n                  T cell states, and show that tethering TFs enables the rational engineering of cell state identity for cell and gene therapies.\n                <\/jats:p>","DOI":"10.64898\/2026.04.20.718569","type":"posted-content","created":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T05:30:15Z","timestamp":1776922215000},"source":"Crossref","is-referenced-by-count":3,"title":["Transcription factor collaboration enables precise T cell state engineering"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6415-7881","authenticated-orcid":false,"given":"Rachel E.","family":"Savage","sequence":"first","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Epigenomics Program, Biology of Adversity Project, Broad Institute of MIT and Harvard, Cambridge, MA 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5595-1450","authenticated-orcid":false,"given":"Christian D.","family":"McRoberts Amador","sequence":"additional","affiliation":[{"name":"Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708"},{"name":"Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2722-2399","authenticated-orcid":false,"given":"Conrad T.","family":"Hock","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Epigenomics Program, Biology of Adversity Project, Broad Institute of MIT and Harvard, Cambridge, MA 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruochi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Epigenomics Program, Biology of Adversity Project, Broad Institute of MIT and Harvard, Cambridge, MA 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8577-1706","authenticated-orcid":false,"given":"Hung-Che","family":"Kuo","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Epigenomics Program, Biology of Adversity Project, Broad Institute of MIT and Harvard, Cambridge, MA 02142"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aretha R.","family":"Gao","sequence":"additional","affiliation":[{"name":"Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708"},{"name":"Department of Biology, Duke University, Durham, NC 27708"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3875-871X","authenticated-orcid":false,"given":"Max A.","family":"Horlbeck","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Harvard Medical School Department of Genetics, Boston, MA 02115"},{"name":"Boston Children\u2019s Hospital Division of Genetics and Genomics, Boston, MA 02115"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1478-4013","authenticated-orcid":false,"given":"Charles A.","family":"Gersbach","sequence":"additional","affiliation":[{"name":"Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708"},{"name":"Department of Biomedical Engineering, Duke University, Durham, NC 27708"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9958-3987","authenticated-orcid":false,"given":"Jason D.","family":"Buenrostro","sequence":"additional","affiliation":[{"name":"Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138"},{"name":"Epigenomics Program, Biology of Adversity Project, Broad Institute of MIT and Harvard, Cambridge, MA 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