Extended Data Fig. 4: Association of TBX21 expression with clonality and cell subsets.
(a) Differential expression of transcription factors with altered activity in CMV seropositivity in baseline CD8+ samples, y-axis shows Benjamini-Hochberg-corrected -log10(Padj.) derived from negative binomial Wald test using CMV- samples as a reference (n = 111 CMV-, n = 95 CMV+). (b) Correlation of transcription factors with induced activity in CMV seropositivity with CMV score (n = 181, Spearman’s Rank Correlation test, rho denotes the Spearman rho, and P value is from two-sided t-test) post cycle 1. (c) TBX21 correlation with with number of CD8+ clones stratified by repertoire occupancy post one cycle of immunotherapy (n = 180, Spearman’s Rank Correlation test, rho and P value as defined in (b)). (d) UMAP plot of CD8+ T-cell subsets in single-cell RNA-seq data. (e) Differential expression of log-transformed cell subset marker genes in single-cell data. (f) Feature plot of TBX21 expression in single-cell data. (g) TBX21 expression dynamics in putative CMV-reactive effector clones in scRNA-seq data, stratified by CMV status (n = 7 CMV+: P = 0.34, n = 8 CMV-: P = 0.16; two-sided Wilcoxon signed-rank test; lower and upper box hinges represent the 25th to 75th percentiles, the central line represents the median and the whiskers extend to the highest and lowest values no greater than 1.5 × interquartile range).
