BATF Knockout in CAR T Cells Prevents Exhaustion in Solid Tumors

Chimeric antigen receptor (CAR) T cells can provide remarkable clinical benefit in several hematologic malignancies, but efforts to apply this therapy to solid tumors have been limited in part by the exhaustion of T cells due to chronic antigen stimulation and immunosuppressive microenvironments. To understand the molecular mechanisms that promote CAR T-cell exhaustion, Zhang, Zhang, Qiao, and colleagues developed an exhaustion model in which CAR T cells targeting the tumor-associated antigen mesothelin (MSLN) were cocultured with MSLN⁺ cancer cell lines at different effector-to-target (E:T) ratios. While an E:T ratio of 2:1 for 24 hours induced effective CAR-T activation, coculture for 7 days at an E:T ratio of 0.1:1 led to the emergence of hypofunctional CAR T cells with an exhaustion-like phenotype. A candidate gene screen was then performed using this hypofunction model of exhaustion, which led to the identification of the transcription factor BATF as a driver of T-cell exhaustion. BATF knockout in CAR T cells enhanced tumor cell lysis in vitro while transcriptionally upregulating T-cell activation–associated pathways and downregulating T-cell exhaustion–related genes. Whereas control anti-MSLN CAR T cells merely slowed tumor growth in multiple cell line–derived xenograft and patient-derived xenograft murine models, treatment with BATF-knockout anti-MSLN CAR T cells enhanced CAR T-cell tumor infiltration, increased IFNγ expression, and led to tumor regression. Notably, BATF editing consistently enhanced efficacy across multiple CAR T-cell designs. Analysis of chromatin immunoprecipitation sequencing and RNA sequencing demonstrated that BATF directly bound to and upregulated a significant portion of T-cell exhaustion–related genes, including PDCD1, the gene that encodes the inhibitor receptor PD-1. Moreover, BATF was also shown to bind multiple effector-related genes, including RUNX3, KLRG1, and TBX21, and subsequent BATF knockout in anti-MSLN CAR T cells shifted the in vivo CAR T-cell population toward a larger proportion of central memory T cells. In summary, these results reveal an important regulator of T-cell exhaustion that may inform CAR T-cell engineering.

Zhang X, Zhang C, Qiao M, Cheng C, Tang N, Lu S, et al. Depletion of BATF in CAR-T cells enhances antitumor activity by inducing resistance against exhaustion and formation of central memory cells. Cancer Cell 2022 Oct 13 [Epub ahead of print].

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