Extended Data Fig. 7: Validation of immune groups in an independent cohort of LARC tumors from TCGA.

Validation of results using an independent cohort of 42 LARC samples from TCGA. (a) Unsupervised hierarchical clustering of pMMR/MSS tumors using ssGSEA scores for a set of well established immune signatures reveals three groups with increasing levels of overall immune infiltrate (IG1–IG3). dMMR/MSI tumors were added later as a fourth group (IG4). (b) Tumors in IG4 had higher TMB and had lower FGA than tumors in the IG1–IG3 groups. Sample sizes for each group are as follows: IG1 (n = 16), IG2 (n = 17), IG3 (n = 7), and IG4 (n = 2). Boxplots’ center lines indicate medians, edges indicate the interquartile range, and the whiskers extend to the highest and lowest values not considered outliers. (c) Distribution of CMS classes across immune groups. (d) Selected significant differences in ssGSEA scores for specific immune cell types across immune groups. Sample sizes for each group are as follows: IG1 (n = 16), IG2 (n = 17), IG3 (n = 7), and IG4 (n = 2). (e) Comparison of expression levels for genes encoding proteins involved in immune checkpoint blockade. Sample sizes for each group are as follows: IG1 (n = 16), IG2 (n = 17), IG3 (n = 7), and IG4 (n = 2). In panels (D) and (E), statistical significance was assessed using a two-sided Mann–Whitney U-test. P values were corrected using the Bonferroni method and significant results are denoted as *q < 0.05, **q < 0.01, ***q < 0.005 and ****q < 0.001. Boxplots’ center lines indicate medians, edges indicate the interquartile range, and the whiskers extend to the highest and lowest values not considered outliers.