STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets

Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8(+) cells, CD4(+) Th1 cells, and T reg cells. In addition, large amounts of paired TCR alpha/beta sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti-PD-1 treatment in MC38 and B16F10 tumor models.

Automated summary

Single-cell RNA sequencing was utilized to analyze T cell subsets and activation states, revealing differences and similarities between human and mouse tumors. The identification of specific T reg cell markers and therapeutic strategies, such as CCR8 depletion, showed potential benefits in tumor treatment and combination therapies with anti-PD-1 treatment in various tumor models.