This study investigates the clonal T cell response to checkpoint blockade therapy in patients with basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Using single-cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing, the researchers analyzed 79,046 cells from matched tumors before and after anti-PD-1 therapy. They found that clonal expansions of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion, were observed. However, these expansions did not arise from pre-existing tumor-infiltrating lymphocytes (TILs) but were composed of novel clonotypes not previously detected in the same tumor. Clonal replacement of T cells was preferentially seen in exhausted CD8+ T cells and was evident in both BCC and SCC patients. The study suggests that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and the T cell response to checkpoint blockade is derived from a distinct repertoire of T cell clones that may have recently entered the tumor.This study investigates the clonal T cell response to checkpoint blockade therapy in patients with basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Using single-cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing, the researchers analyzed 79,046 cells from matched tumors before and after anti-PD-1 therapy. They found that clonal expansions of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion, were observed. However, these expansions did not arise from pre-existing tumor-infiltrating lymphocytes (TILs) but were composed of novel clonotypes not previously detected in the same tumor. Clonal replacement of T cells was preferentially seen in exhausted CD8+ T cells and was evident in both BCC and SCC patients. The study suggests that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and the T cell response to checkpoint blockade is derived from a distinct repertoire of T cell clones that may have recently entered the tumor.