Immune evasive characteristics of the KRAS mutant colorectal cancer tumor microenvironment

Background: Recent clinical trials have indicated that KRAS mutant colorectal cancer (CRCs) are more resistant to combination immunotherapy approaches compared to KRAS wild-type (WT) microsatellite stable (MSS) CRCs, potentially related to an immune suppressive tumor microenvironment (TME). Here, we investigate the TME of MSS KRAS mutant CRCs to characterize the immune-related signaling pathways and factors that modulate the immune evasive TME associated with KRAS mutant CRCs. Methods: A gene-set enrichment analysis (GSEA) on the Colorectal Adenocarcinoma (TCGA, PanCancer Atlas) dataset was performed to identify differential gene expression patterns between patients with MSS CRCs with or without a KRAS mutation. A second GSEA analysis explored RNA expression data from the NCI Patient-Derived Models Repository (PDMR) database of matched patient organoid and whole tumor samples from KRAS mutant and WT CRCs. Results: A total of 496 MSS CRC subjects were identified in the TCGA dataset. KRAS mutant CRCs (195) were compared to a WT cohort consisting of patients lacking a KRAS, NRAS, or BRAF mutation (255). KRAS enriched gene sets (FDR q-value<0.25) included hallmark mitotic spindle, p53 pathway, glycolysis, oxidative phosphorylation, reactive oxygen species pathway, and estrogen response late. The WT cohort had enrichment of immune-related gene sets, including hallmark allograft rejection, inflammatory response, and IL6 JAK STAT3 signaling. Significantly expressed genes (q-value<0.05) in the KRAS enriched gene sets were involved in TGF-beta signaling (TGFB1 (Log2FC: 0.85), EPHA2 (0.4), KLK11 (1.47), INHBE (0.51)), M2-macrophage recruitment (KLK10 (1.24), CA12 (0.75), KLK8 (0.79), and immune exclusion (CD44(0.35), LAMC2 (0.43), KLK8 (0.79), NT53/CD73 (0.66)). Genes upregulated in the WT cohort were associated with immune cell activation and T-cell regulation (GZMB (0.83), MERTK (0.66), PROCR (0.59), CD40 (0.48)), M1-macrophages (AK4 (0.65)), and immune infiltration (SPAG4 (0.49)). RNA expression data from the PDMR database was analyzed from patients with APC and TP53 mutations with or without a KRAS mutation (three patients/cohort). GSEA revealed that immune-related gene sets were significantly enriched in WT tumors including interferon gamma/alpha response, TNFA signaling via NFKB, complement, allograft rejection, and inflammatory response. When immune TME signaling was isolated by separating gene expression present in the organoid data from the original tumor samples, similar results were observed. Conclusion: KRAS mutant CRCs are characterized by an immune suppressive TME. Further analysis of the pathways and genes driving this phenotype will help identify actionable therapeutic targets to improve immunotherapy responses for these patients.