Extended Data Fig. 2: Patients with STK11 mutated tumors in the SBRT and control arms show no difference in upregulation of immune programs or T cell expansion.
(a) We did not observe significant upregulation of immune response related gene sets in on-therapy tumors among patients with STK11 mutations in the SBRT arm (n = 5 samples) versus the control arm (n = 5 samples). (b) Among patients with STK11 mutations, cellular proliferation and cell cycle progression gene sets were significantly more downregulated in on-therapy tumors in the SBRT (n = 5 samples) compared to the control arm (n = 5 samples; E2f targets, GSEA (two-sided) FDR-adjusted P = 1.62e-10, NES = −2.33; g2m checkpoint, GSEA (two-sided) FDR-adjusted P = 6.14e-7, NES = −2.07). (c, d) There were no significant differences in T cell expansion between patients with STK11 mutations in the SBRT (n = 4 samples) and control (n = 5 samples) arms for all clones (c) or only newly expanded clones (d) (Mann-Whitney U test, two-sided). While limited by the small number of STK11-mutant tumors per arm, these findings do not support an enhancement of anti-tumor immune responses in the SBRT arm compared to the control arm for tumors harboring STK11 mutations. Box plots depict the median value and hinges correspond to the first and third quartiles. The whiskers extend from the corresponding hinge to the furthest value within 1.5* the interquartile range from the hinge.
