Extended Data Fig. 7: Comparison of transcriptomic features between patient subgroups and flow cytometry validation of differentially expressed markers.
a, Comparing tumor-reactive TIL transcriptomic features between CB vs NB patients, differentially expressed genes were selected by using a non-biased selection criteria: P < 0.05 & fold change ≥2× for CD8 T cells and P < 0.05 & fold change ≥1.7× for CD4 T cells. Transcriptomic expression of those genes in bulk CD4+ and CD8+ TIL was plotted for a side-by-side comparison. ns: not significant between CB vs NB patients. b, Tetramers loading MEX3D & NUP133 neoAg epitopes for PT03 and TP53 & KRAS neoAg epitopes for PT31 were used to gate neoantigen-specific TIL. Stained differentially expressed markers were labeled on the bottom. The number on the upper right corner of each histogram shows the median fluorescence intensity for the indicated marker. Corresponding FMOs are shown in the top row. #, CD8 BV605 was used instead of CD8 FITC for detecting perforin expression. c, Flow cytometry analysis detecting surface CD39/CD69 expression in CD4+ and CD8+ TIL. Two-sided Mann–Whitney U-test was performed to compare Clinical Benefit (n = 6 TIL samples) vs No-Benefit groups (n = 10 TIL samples) with no statistical significance. Bars indicate mean ± SD. Gating strategy was shown in Supplementary Information. d, Single-cell transcriptomic analysis showing expression of Tscm and Tex signature genes in tumor-reactive CD8+TIL between Clinical Benefit (CB) vs No-Benefit (NB) groups. e, Gene Set Enrichment Analysis (GSEA) raw data for Fig. 2f.
