Intratumoral CD8+ T cells with a tissue-resident phenotype mediate local immunity and immune checkpoint responses in breast cancer

CD8+ tumor-infiltrating lymphocytes with a tissue-resident memory T (TRM) cell phenotype are associated with favorable prognosis in patients with triple negative breast cancer (TNBC). However, the relative contribution of CD8+ TRM cells to anti-tumor immunity and immune checkpoint blockade efficacy in breast cancer remains unknown. Here, we show that intratumoral CD8+ T cells in murine mammary tumors transcriptionally resemble those from triple-negative breast cancer patients. Phenotypic and transcriptional studies established two intratumoral sub-populations: one more enriched in markers of terminal exhaustion (TEX-like) and the other with a bona-fide resident phenotype (TRM-like). Treatment with anti-PD-1 and anti-CTLA-4 therapy resulted in a expansion of these intratumoral populations, with the TRM-like subset displaying significantly enhanced cytotoxic capacity. Importantly, we demonstrate that it is the TRM-like CD8+ T cells can provide local immune protection against mammary tumor re-challenge and that a gene signature from remaining TRM-like CD8+ T cells extracted from tumor-free tissue was significantly associated with improved outcomes in human TNBC patients treated with checkpoint inhibition. Overall, our data suggest that CD8+ T cells with a tissue resident phenotype play a critical role in response to local immunosurveillance and responses to immune checkpoint blockade in breast cancer FACS purified CD8+ T cell subsets were processed for RNA using the RNeasy mini kit (Qiagen) as per the manufacturer's instructions. RNA TapeStation (Agilent, USA) analysis was performed as per the manufacturer's instructions to assess the quantity and quality of RNA material isolated from TNBC tumors. 10ng total RNA was used for library preparation according to manufacturer’s instructions (QuantSeq 3' mRNA-Seq FWD, Lexogen). Indexed libraries were pooled and sequenced on a NextSeq500 (Illumina). The library was then amplified with 3’ PCR primers containing sample indices and the Illumina clustering guides. Five to ten million single-end 75 bp reads were generated as an output.