SSN-seq: Multiplexed single-cell transcriptomic profiling via genetic barcoding with shielded small nucleotides

To facilitate scalable longitudinal profiling of single cells we developed a universal permanent genetic cell barcoding technology based on the expression of shielded small nucleotides coupled with single-cell RNA-seq (SSN-seq). SSN barcodes are highly expressed and contain direct-capture sequences to enable recovery of distinct barcodes directly in each single-cell transcriptome allowing cell identity history to be recorded over time, in parallel with cell identity. SSN-seq is compatible with both 3' and 5' single-cell profiling and is readily adaptable to numerous cell types including human primary T cells and CAR T cells making it a promising tool for rapidly improving adoptive cell therapies and expanding their functionality. We applied SSN-seq to track the dynamics of CAR T cell states at the time of infusion and upon isolation from in vivo tumor rechallenge model. Our study identified that a novel combination of cytokines and small molecule inhibitors used for CAR T cells manufactured ex vivo, promotes the expansion of persistent CD4+ memory T cell populations in vivo. Together, these results demonstrate the utility of our method for multiplexed perturbation experiments that reveal the dynamics of cell states over time, with a high degree of confidence. Overall design: scRNA-seq of SSN-barcoded cells in vitro and in vivo