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Zhu Z, Lou G, Teng XL, Wang H, Luo Y, Shi W, Yihunie K, Hao S, DeGolier K, Liao C, Huang H, Zhang Q, Fry T, Wang T, Yao C, Wu T. FOXP1 and KLF2 reciprocally regulate checkpoints of stem-like to effector transition in CAR T cells. Nat Immunol 2024; 25:117-128. [PMID: 38012417 PMCID: PMC10841689 DOI: 10.1038/s41590-023-01685-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 10/16/2023] [Indexed: 11/29/2023]
Abstract
In cancer and infections, self-renewing stem-like CD8+ T cells mediate the response of immunotherapies and replenish terminally exhausted T cells and effector-like T cells. However, the programs governing the lineage choice in chimeric antigen receptor (CAR) T cells are unclear. Here, by simultaneously profiling single-cell chromatin accessibility and transcriptome in the same CAR T cells, we identified heterogeneous chromatin states within CD8+ T cell subsets that foreshadowed transcriptional changes and were primed for regulation by distinct transcription factors. Transcription factors that controlled each CD8+ T cell subset were regulated by high numbers of enhancers and positioned as hubs of gene networks. FOXP1, a hub in the stem-like network, promoted expansion and stemness of CAR T cells and limited excessive effector differentiation. In the effector network, KLF2 enhanced effector CD8+ T cell differentiation and prevented terminal exhaustion. Thus, we identified gene networks and hub transcription factors that controlled the differentiation of stem-like CD8+ CAR T cells into effector or exhausted CD8+ CAR T cells.
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Affiliation(s)
- Ziang Zhu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Immunology Ph.D. Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guohua Lou
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xiao-Lu Teng
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Haixia Wang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ying Luo
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wangke Shi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kiddist Yihunie
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shumeng Hao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kole DeGolier
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huocong Huang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Terry Fry
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chen Yao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tuoqi Wu
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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