Transcription factor collaboration enables precise T cell state engineering.
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| Abstract | Transcription factors (TFs) collaborate to regulate gene expression programs that define cell fate. In CD8 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 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 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 "master collaborator", 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 T cell states, and show that tethering TFs enables the rational engineering of cell state identity for cell and gene therapies. |
| Year of Publication | 2026
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| Journal | bioRxiv : the preprint server for biology
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| Date Published | 04/2026
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| ISSN | 2692-8205
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| DOI | 10.64898/2026.04.20.718569
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| PubMed ID | 42079248
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