Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis
TRZUPEK D., DUNSTAN M., CUTLER A., Lee M., GODFREY L., ASCHENBRENNER D., UHLIG H., WICKER L., TODD J., CORREIA BOTELHO CHAVES FERREIRA R.
Background Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA-sequencing (scRNA-seq) and antibody-based cytometry. Here we present a multi-omics approach allowing the simultaneous targeted quantification of mRNA and protein expression in single-cells and investigate its performance to dissect the heterogeneity of human immune cell populations. Methods We have quantified the single-cell expression of 397 genes at the mRNA level and up to 68 proteins using oligo-conjugated antibodies (AbSeq) in 43,656 primary CD4+ T cells isolated from blood and 31,907 CD45+ cells isolated from blood and matched duodenal biopsies. We explored the sensitivity of this targeted scRNA-seq approach to dissect the heterogeneity of human immune cell populations and identify trajectories of functional T-cell differentiation. Results We provide a high-resolution map of human primary CD4+ T cells, and identify precise trajectories of Th1, Th17 and regulatory T-cell (Treg) differentiation in blood and tissue. The sensitivity provided by this multi-omics approach identified the expression of the B7 molecules CD80 and CD86 on the surface of CD4+ Tregs, and we further demonstrated that B7 expression has the potential to identify recently activated T cells in circulation. Moreover, we identified a rare subset of CCR9+ T cells in blood with tissue-homing properties and expression of several immune checkpoint molecules, suggestive of a regulatory function. Conclusions This transcriptomic and proteomic hybrid technology provides a cost-effective solution to dissect the heterogeneity of immune cell populations, including more precise and detailed descriptions of the differentiation and activation of circulating and tissue-resident cells in response to therapies and in stratification of patients.