Integrated BATF transcriptional network regulates suppressive intratumoral regulatory T cells.

Human regulatory T cells (T) are crucial regulators of tissue repair, autoimmune diseases, and cancer. However, it is challenging to inhibit the suppressive function of T for cancer therapy without affecting immune homeostasis. Identifying pathways that may distinguish tumor-restricted T is important, yet the transcriptional programs that control intratumoral T gene expression, and that are distinct from T in healthy tissues, remain largely unknown. We profiled single-cell transcriptomes of CD4 T cells in tumors and peripheral blood from patients with head and neck squamous cell carcinomas (HNSCC) and those in nontumor tonsil tissues and peripheral blood from healthy donors. We identified a subpopulation of activated T expressing multiple tumor necrosis factor receptor (TNFR) genes (TNFR T) that is highly enriched in the tumor microenvironment (TME) compared with nontumor tissue and the periphery. TNFR T are associated with worse prognosis in HNSCC and across multiple solid tumor types. Mechanistically, the transcription factor BATF is a central component of a gene regulatory network that governs key aspects of TNFR T. CRISPR-Cas9-mediated knockout in human activated T in conjunction with bulk RNA sequencing, immunophenotyping, and in vitro functional assays corroborated the central role of BATF in limiting excessive activation and promoting the survival of human activated T. Last, we identified a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral T in patients with HNSCC. These findings uncover a primary transcriptional regulator of highly suppressive intratumoral T, highlighting potential opportunities for therapeutic intervention in cancer without affecting immune homeostasis.