A microRNA-regulated transcriptional state defines intratumoral CD8+T cells that respond to immunotherapy

Rising rates of advanced-stage colorectal cancer (CRC) and poor survival rates necessitate effective therapeutic options. Immune checkpoint inhibition (ICI), specifically anti-PD-1 therapy, shows potential, but clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8 T cell infiltrated tumors through an unbiased in vivo Crispr-Cas9 screen of tumor-antigen-specific CD8 T cell-related miRNAs. MiR-155 was necessary for a vital CD8 T cell differentiation cascade by repressing Ship-1, thereby inhibiting stemness and Tcf-1 while enhancing effector function and Cxcr6 expression, an indispensable aspect of anti-tumor and -PD-1 responses. Through a miR-155-dependent CD8 T cell transcriptional profile, we identified a gene signature that predicts anti-PD-1 responses across ten cancers. Taken together, our findings support a model whereby miR-155 serves as a central axis for CD8 T cell-dependent immunity in CRC and anti-PD-1 responses against multiple cancers that may be leveraged therapeutically or as a biomarker. Overall design: To analyze the effects of miR155 on T cell states within colon cancer, we performed single-cell RNA-Seq (scRNAseq) on CD45+ immune cells isolated by FACS from MC38-challenged WT or miR-155 TKO mice with or without anti-PD-1 mAb treatment. There were 8 mouse treatment conditions. All mice, both males and females, were challenged with MC38 tumors. Half of each sex cohort contained miR155 fl/fl with a CD4-Cre driver, the other half had only the miR155 fl/fl allele. Half of the mice within each of these genotypes received anti-PD-1 injections, the other half received a PBS mock injection. Each sample set was pooled from tumors in 6 to 8 mice within each of the 8 treatment conditions.