Single cell T cell receptor clonality and functinonal state in infusion products. (A) Proportion of CD8 T cells in IPs of Rs (pink) vs NRs (blue) by scRNA-seq. (B) Proportion of CD8 TEM cells in IPs of Rs (pink) vs NRs (blue) by scRNA-seq. (C) Proportion of sets of clonally expanded cells (“clonotypes”) in IPs that have majority CD8 TEM phenotypes of R (pink) vs NR (blue) by scRNA-seq. Cells are considered clonally expanded if there are >2 cells sharing the same TCR CDR3 sequence. (D) Scatterplot of T-cell clonotypes of Rs (pink) and NRs (blue) by subset: CD4 (left) or CD8 (right) and more effector memory (upward arrow) vs less effector memory/more central memory (downward arrow). The CD4 vs CD8 score is computed as the difference between mean normalized CD8A gene expression and mean normalized CD4 gene expression among the cells in each clonotype. The effector memory score is computed as the mean normalized expression of the genes GZMA, GZMB, GZMH, GZMK, GZMM, PRF1, GNLY, IFNG, and TNF in each clonotype. Up to the largest 25 clones for each patient are shown. (E-F) Histograms of top expanded T-cell clones and their respective T-cell subsets for 4 representative Rs (E) and NRs (F). In the x-axis, each bar represents an individual clone; y-axis, number of members of each clone (“count”). CD8 TEM are shown in purple. (G) Differential gene expression analysis of clonally expanded (left) vs nonclonally expanded (right) CD8 TEM cells in the IP, pseudobulked, and normalized by patient and labeled subset. Patients with <30 cells of either clonally expanded or nonclonally expanded CD8 TEM cells were excluded. Treg, regulatory T-cell.
