Expanding the split-pool combinatorial barcoding toolkit to characterize the effects of aging in mouse TCR diversity.

Abstract We recently released a flexible and high throughput single-cell sequencing method that leverages split-pool combinatorial barcoding to simultaneously profile the whole transcriptome and T cell receptor (TCR) sequences of up to 1 million human T cells from up to 96 samples. This technology is able to recover reproducibly paired TCR sequences in the majority of assayed T cells across different sample types (CAR-Ts, culture activated T cells, etc). Here, we report on the extension of our method to be able to recover the immune repertoire and gene expression profiles from mouse T cells. We use our assay to characterize TCR diversity changes during the mouse lifecycle. Specifically, we profile hundreds of thousands of mouse spleen-resident T cells at different stages of life. We perform transcriptome-based clustering and demonstrate that this approach identifies all major T cell populations (CD4+, CD8+, Tregs, etc.) while efficiently detecting paired TCR sequences. Furthermore, consistent with previous findings, we show differences in clonotype diversity that correlate with age. Overall, we present an extension of our TCR technology that allows for the characterization of mouse TCR sequences and showcases its utility in studying the effects of aging in TCR repertoire diversity. We envision our method will help researchers gain additional insights in mouse models of autoimmune and infectious diseases, as well as cancer.