Germline Variants of CYBA and TRPM4 Predispose to Familial Colorectal Cancer

Abstract

Familial colorectal cancer (CRC) is only partially explained by known germline predisposing genes. We performed whole-genome sequencing in 15 Polish families of many affected individuals, without mutations in known CRC predisposing genes. We focused on loss-of-function variants and functionally characterized them. We identified a frameshift variant in the <i>CYBA</i> gene (c.246delC) in one family and a splice site variant in the <i>TRPM4</i> gene (c.25-1 G > T) in another family. While both variants were absent or extremely rare in gene variant databases, we identified four additional Polish familial CRC cases and two healthy elderly individuals with the <i>CYBA</i> variant (odds ratio 2.46, 95% confidence interval 0.48-12.69). Both variants led to a premature stop codon and to a truncated protein. Functional characterization of the variants showed that knockdown of <i>CYBA</i> or <i>TRPM4</i> depressed generation of reactive oxygen species (ROS) in LS174T and HT-29 cell lines. Knockdown of <i>TRPM4</i> resulted in decreased MUC2 protein production. <i>CYBA</i> encodes a component in the NADPH oxidase system which generates ROS and controls, e.g., bacterial colonization in the gut. Germline <i>CYBA</i> variants are associated with early onset inflammatory bowel disease, supported with experimental evidence on loss of intestinal mucus barrier function due to ROS deficiency. <i>TRPM4</i> encodes a calcium-activated ion channel, which, in a human colonic cancer cell line, controls calcium-mediated secretion of MUC2, a major component of intestinal mucus barrier. We suggest that the gene defects in <i>CYBA</i> and <i>TRPM4</i> mechanistically involve intestinal barrier integrity through ROS and mucus biology, which converges in chronic bowel inflammation.