Clonally expanded EOMES⁺ Tr1-like cells in primary and metastatic tumors are associated with disease progression

Regulatory T (T_reg) cells are a barrier for tumor immunity and a target for immunotherapy. Using single-cell transcriptomics, we found that CD4⁺ T cells infiltrating primary and metastatic colorectal cancer and non-small-cell lung cancer are highly enriched for two subsets of comparable size and suppressor function comprising forkhead box protein P3⁺ T_reg and eomesodermin homolog (EOMES)⁺ type 1 regulatory T (Tr1)-like cells also expressing granzyme K and chitinase-3-like protein 2. EOMES⁺ Tr1-like cells, but not T_reg cells, were clonally related to effector T cells and were clonally expanded in primary and metastatic tumors, which is consistent with their proliferation and differentiation in situ. Using chitinase-3-like protein 2 as a subset signature, we found that the EOMES⁺ Tr1-like subset correlates with disease progression but is also associated with response to programmed cell death protein 1-targeted immunotherapy. Collectively, these findings highlight the heterogeneity of T_reg cells that accumulate in primary tumors and metastases and identify a new prospective target for cancer immunotherapy.