Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells

Single-cell RNA sequencing in principle offers unique opportunities to improve the efficacy of contemporary T-cell based immunotherapy against cancer. The use of high-quality single-cell data will aid our incomplete understanding of molecular programs determining the differentiation and functional heterogeneity of cytotoxic T lymphocytes (CTLs), allowing for optimal therapeutic design. So far, a major obstacle to high depth single-cell analysis of CTLs is the minute amount of RNA available, leading to low capturing efficacy.

To overcome this, researchers from the Technical University of Munich have tailored a droplet-based approach for high-throughput analysis (tDrop-seq) and a plate-based method for high-performance in-depth CTL analysis (tSCRB-seq). The latter gives, on average, a 15-fold higher number of captured transcripts per gene compared to droplet-based technologies. The improved dynamic range of gene detection gives tSCRB-seq an edge in resolution sensitive downstream applications such as graded high confidence gene expression measurements and cluster characterization. The researchers demonstrate the power of tSCRB-seq by revealing the subpopulation-specific expression of co-inhibitory and co-stimulatory receptor targets of key importance for immunotherapy.

Schematic protocol representation of SCRB-seq and Drop-seq

(A) Schematic representation of the P14 experimental system. The green, blue and red colour denote naïve P14 T cells, P14 T cells recovered at day 8 post LCMV Armstrong infection and P14 T cells recovered at day 40 post LCMV clone-13 infection respectively. (B) Illustrates the difference in the single-cell capturing strategy of SCRB-seq versus Drop-seq. (C) Representation of the common chemistry downstream of single-cell capturing.