KRAS mutation and Consensus Molecular Subtypes 2 and 3 are independently associated with reduced immune infiltration and reactivity in colorectal cancer

PURPOSE: KRAS mutation is a common canonical mutation in CRC, found at differing frequencies in all Consensus Molecular Subtypes (CMS). The independent immunobiological impacts of RAS mutation and CMS are unknown. Thus, we explored the immunobiological effects of KRAS mutation across the CMS spectrum.

EXPERIMENTAL DESIGN: Transcriptional analysis of immune genes/signatures was performed with RNA-seq using The Cancer Genome Atlas (TCGA) and the KFSYSCC data set. Multivariate analysis included KRAS status, CMS, tumour location, MSI status, and neoantigen load. Protein expression of STAT1, HLA-Class II, and CXCL10 was analysed by digital immunohistochemistry.

RESULTS: The Th1-centric co-ordinated immune response cluster (CIRC) was significantly, albeit modestly, reduced in KRAS mutant CRC in both data sets. Cytotoxic T cells, neutrophils and the interferon gamma pathway were suppressed in KRAS mutant samples. The expression of STAT1 and CXCL10, were reduced at the mRNA and protein levels. In multivariate analysis KRAS mutation, CMS2 and CMS3 were independently predictive of reduced CIRC expression. Immune response was heterogeneous across KRAS mutant CRC: CMS2 KRAS mutant samples have the lowest CIRC expression, reduced expression of the interferon gamma pathway, STAT1 and CXCL10 and reduced infiltration of cytotoxic cells and neutrophils relative to CMS1 and CMS4 and to CMS2 KRAS wild type samples in the TCGA. These trends held in the KFSYSCC data set.

CONCLUSIONS: KRAS mutation is associated with suppressed Th1/cytotoxic immunity in CRC, the extent of the effect being modulated by CMS subtype. These results add a novel immunobiological dimension to the biological heterogeneity of CRC.