Extended Data Fig. 4: Changes in genomic and transcriptomic features on therapy. | Nature Cancer

Extended Data Fig. 4: Changes in genomic and transcriptomic features on therapy.

From: Highly aneuploid non-small cell lung cancer shows enhanced responsiveness to concurrent radiation and immune checkpoint blockade

Extended Data Fig. 4

(a) Clonal evolution of somatic mutations on treatment. Each box corresponds to an individual patient. Axes indicate the variant allele fractions (VAFs) of each mutation (x-axis: pre-treatment; y-axis: on-treatment); oncogenic mutations highlighted in blue; (n = 18 patients). (b) Differences in on-treatment density of (TTF1+/CK5+) tumor cells as determined by mIF between treatment arms; (SBRT n = 6 patients, SBRT+Ipi/Nivo n = 6 patients); two-sided Wilcoxon test. The top and bottom edges represent the 1st and 3rd quartiles, respectively; the center line represents the median; whiskers extend to the farthest data points which do not represent outliers (within 1.5x the interquartile range); outliers are plotted as points above and below the box-and-whisker plot. (c) On treatment changes in purity and ploidy; two-sided paired Wilcoxon test. Patient #12 was excluded from the SBRT+ipi/nivo group because the tumor purity could not accurately be determined for the on-treatment sample (SBRT+Ipi/Nivo n = 7 patients, SBRT n = 10 patients). Boxplot elements are defined in the legend of panel b. (d) Changes in ssGSEA Hallmark pathway scores on-treatment (SBRT n = 8 patients, SBRT+Ipi/Nivo n = 7 patients); two-sided paired Wilcoxon P<0.05 are highlighted in blue. (e) Plots illustrating patient-level changes in ssGSEA Hallmark pathways determined to be significantly differentially changed between treatment arms (see Fig. 2d); (SBRT n = 8 patients, SBRT+Ipi/Nivo n = 7 patients); two-sided paired Wilcoxon test. Box plot elements are defined in the legend of panel b. (f) Changes in ESTIMATE stromal score on treatment in each treatment arm; (SBRT n = 8 patients, SBRT+Ipi/Nivo n = 7 patients); two-sided paired Wilcoxon test. Box plot elements are defined in the legend of panel b.

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