A single-cell proteomic and transcriptomic assay identifies genes related to polyfunctionality of CAR-T cells targeting GPC1 in pancreatic cancer

To understand the molecular determinants of CAR-T cell polyfunctionality, we simultaneously measured the protein and RNA expression levels of 23 single CD8+ D4-IgG4H-CD28TM CAR T cells targeting GPC1 stimulated with T3M4 pancreatic cancer cells. We identified two CAR-T clusters, low polyfunctionality and high polyfunctionality subsets, in a 2D t-SNE plot. Moreover, our single-cell mRNA expression profiling revealed 23 genes that displayed statistically significant, concordant differences between the two cell subsets. D4-IgG4H-CD28TM CAR-T cells targeting GPC1 were stimulated with T3M4 pancreatic cancer cells, then grouped into high-polyfunctionality and low-polyfunctionality subsets based on the cytokine secretion profile. Then scRNA-seq was used to analyze upregulated genes in each subset.