Knocking out BATF improves CAR-T cell efficacy by resisting exhaustion and forming central memory cells

Chimeric antigen receptor modified T (CAR-T) cells have achieved remarkable therapeutic efficacy treating various hematologic malignancies. However, CAR-T therapy has not shown robust anti-tumor activity against solid tumor. One of the major challenges is T cell exhaustion. In order to explore the mechanism of CAR-T cell exhaustion, we established a CAR-T cell hypofunction model that shared many functional and molecular features with exhausted T cells isolated from patient tumor samples. We performed a candidate gene screen using this model, and found knocking out transcription factors BATF and IRF4 improved CAR-T cell function in vitro. However, upon testing their efficacy in cell-line-derived xenograft (CDX) and patient tumor-derived xenograft (PDX) mouse models, only genetic depletion of BATF improved CAR-T cell efficacy in vivo. While BATF has been implicated as an important player in T cell differentiation and exhaustion, its role in CAR-T cells and the underlying mechanism are still elusive. Here we performed Chromatin immunoprecipitation (CHIP) and RNA seq experiments in CAR-T cells and found that BATF bound to and up-regulated a subset of T cell exhaustion genes and down-regulated memory T cell differentiation-associated genes. Furthermore, knocking out BATF endows CAR-T cells with improved resistance to exhaustion and more central memory cells. Therefore, we conclude that BATF is a key factor limiting CAR-T cell function, and its depletion improves CAR-T cells efficacy against solid tumor.