Chronic antigen in solid tumors drives a distinct program of T cell residence

Analyses of healthy tissue reveal signatures that identify resident memory CD8+ T cells (TRM), which survey tissues without recirculating. The density of TRM-phenotype cells within solid tumors correlates favorably with prognosis, suggesting that intratumoral residents control cancer. However, residence has not been directly tested and intratumoral TRM-phenotype cells could instead reflect aspects of the microenvironment that correlate with prognosis. Using a breast cancer model, we found that conventional TRM markers do not inform the tumor residence of either bystander or tumor-specific cells, which exhibit further distinct phenotypes in the tumor microenvironment and healthy mammary tissue. Rather, tumor-specific, stem-progenitor CD8+ T cells migrate to tumors and become resident while acquiring select markers of exhaustion. These data indicate that tonic antigen stimulation and the tumor environment drive distinct programs of residence compared to healthy tissues and that tumor immunity is sustained by continued migration of tumor-specific stem cells. We performed single-cell RNA sequencing with cellular indexing of transcriptomes and epitopes (CITE-seq) on CD8+ T cells isolated from EO771-ova breast tumors, non-tumor bearing mammary fat pads, and spleens from a pool of nine biologic replicates. Samples include virus-specific Thy1.1+ P14 CD8+ T cells, tumor-specific CD45.1+ OT-I CD8+ T cells, and polyclonal endogenous CD44+CD45.2+CD45.1-Thy1.1- CD8+ T cells.