10X single-cell RNASeq profiling of CD8+ T cells from wildtype MC38 tumors and paired peripheral blood

The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. However, tracking tumor antigen-specific CD8+ T cells in the blood is challenging due to their small number and limited reagents to track these cells. We asked whether paired single-cell RNA and T cell receptor (TCR) sequencing could be used to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors using the TCR as a molecular barcode. By leveraging the transcriptome, we characterized these cells, and identified candidate cell surface markers for to enrich this population. These data show that the TCR can be used to identify tumor-relevant cells for characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells. 10X 5' single cell RNASeq and paired TCR sequencing was performed on sorted CD8+ T cells from wildtype MC38 tumors in C57BL/6 mice, as well as on sorted CD8+ CD44+ T cells from the peripheral blood of paired mice. Using the TCR sequence as a molecular barcode, we identified matching CD8+ T cell clones between the peripheral blood and tumor, and characterized the matching versus non-matching T cell populations within a tissue compartment and between tissue compartments. For some samples, we also performed CITE seq to detect protein expression of CD39, CX3CR1, and NKG2D.