Data from KRAS Mutation and Consensus Molecular Subtypes 2 and 3 Are Independently Associated with Reduced Immune Infiltration and Reactivity in Colorectal Cancer

Abstract

<div>Abstract<p><b>Purpose:</b> <i>KRAS</i> mutation is a common canonical mutation in colorectal cancer, 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 <i>KRAS</i> mutation across the CMS spectrum.</p><p><b>Experimental Design:</b> Expression analysis of immune genes/signatures was performed using The Cancer Genome Atlas (TCGA) RNA-seq and the KFSYSCC microarray datasets. Multivariate analysis included <i>KRAS</i> status, CMS, tumor location, MSI status, and neoantigen load. Protein expression of STAT1, HLA-class II, and CXCL10 was analyzed by digital IHC.</p><p><b>Results:</b> The Th1-centric co-ordinate immune response cluster (CIRC) was significantly, albeit modestly, reduced in <i>KRAS</i>-mutant colorectal cancer in both datasets. Cytotoxic T cells, neutrophils, and the IFNγ pathway were suppressed in <i>KRAS</i>-mutant samples. The expressions of STAT1 and CXCL10 were reduced at the mRNA and protein levels. In multivariate analysis, <i>KRAS</i> mutation, CMS2, and CMS3 were independently predictive of reduced CIRC expression. Immune response was heterogeneous across <i>KRAS</i>-mutant colorectal cancer: <i>KRAS</i>-mutant CMS2 samples have the lowest CIRC expression, reduced expression of the IFNγ pathway, <i>STAT1</i> and <i>CXCL10</i>, and reduced infiltration of cytotoxic cells and neutrophils relative to CMS1 and CMS4 and to <i>KRAS</i> wild-type CMS2 samples in the TCGA. These trends held in the KFSYSCC dataset.</p><p><b>Conclusions:</b> <i>KRAS</i> mutation is associated with suppressed Th1/cytotoxic immunity in colorectal cancer, the extent of the effect being modulated by CMS subtype. These results add a novel immunobiological dimension to the biological heterogeneity of colorectal cancer. <i>Clin Cancer Res; 24(1); 224–33. ©2017 AACR</i>.</p></div>