Single-cell gene expression profile and TyP-HIM-seq DNA barcode level of CD19 CAR-Jurkat and Ramos cells

Cell–cell interactions (CCIs) are essential for tissue functionality and targeted therapies, particularly in the context of chimeric antigen receptor T (CAR T) cells. Here, we introduce TyP-HIM-seq, a barcoding approach based on tyrosinase-catalyzed proximity (TyP) labeling. This method enables the simultaneous high-throughput measurement of interacting cells and their mRNA expressions through single-cell sequencing. By translating intercellular contact into in situ chemical labeling of a DNA barcode, TyP-HIM-seq allows for a comprehensive assessment of CCIs and full deconvolution of related molecular pathways. We used TyP-HIM-seq to investigate the CCIs between CD19 CAR-Jurkat cells and Ramos tumor cells. CAR-J cells and Ramos cells were separately modified with tyrosinase and phenol groups to serve as bait and prey cells. Then, the two cells were mixed at 1:1 and cocultured with amine-ssDNA barcodes at 37 °C for 30 min. After stringent PBS washing, the cells with barcoded DNA tagging were profiled by scRNA-seq.