Fig. 4: pTRC reflect known gene programs of tumor-specific TIL.
A UMAP of TIL in NSCLC colored by clonal size, with max clonal size of 1000, the cells with clonal size over 1000 are colored the same with cells with clonal size of 1000. B Boxplot showing the proportion of pTRC and non-pTRC in tumor tissue. Data are shown as the average of each clone corresponding to pTRC or non-pTRC (clonal size divided by the total number of TIL in each tumor sample), only the non-pTRC with at least 5 TIL were selected. Comparisons were performed at the clonal level using two-sided Wilcoxon rank-sum test. C Top 20 differentially expressed genes in pTRC and non-pTRC based on differential gene expression analysis at the pseudobulk clonal level. D Mean TRM signature score, E checkpoint score, F cytotoxicity score, and G TCR signaling score in pTRC (n = 443) and non-pTRC clones (n = 18,375) in the tumor. Comparisons were performed at the clonal level using two-sided Wilcoxon rank-sum test. H Spearman’s correlation between the ranks of differentially expressed genes in pTRC and non-pTRC vs. differentially expressed genes in functionally validated MANA- and bystander (flu- or EBV-specific) TIL. Genes were ranked by log2 fold change from top (upregulated in pTRC or MANA-specific TIL) to the bottom (downregulated in pTRC or MANA-specific TIL). Box plots represent minima maxima as whiskers, the median as the center line within each box, and the interquartile range (IQR) between 25th and 75th percentiles as the bounds of each box.
