Differential genetic influences over colorectal cancer risk and gene expression in large bowel mucosa: Topographical differences in colorectal cancer risk loci eQTLs

Site-specific variation in colorectal cancer (CRC) incidence, biology and prognosis are poorly understood. We sought to determine whether common genetic variants influencing CRC risk might exhibit topographical differences on CRC risk through regional differences in effects on gene expression in the large bowel mucosa. We conducted a site-specific genetic association study (10,630 cases, 31,331 controls) to identify whether established risk variants exert differential effects on risk of proximal, compared to distal CRC. We collected normal colorectal mucosa and blood from 481 subjects and assessed mucosal gene expression using Illumina HumanHT-12v4 arrays in relation to germline genotype. Expression quantitative trait loci (eQTLs) were explored by anatomical
location of sampling. The rs3087967 genotype (chr11q23.1 risk variant) exhibited significant site-specific effects - risk of distal CRC (OR=1.20, P=8.20x10-20) with negligible effects on proximal CRC risk (OR=1.05, P=0.10). Expression of 1261 genes differed between proximal and distal colonic mucosa (top hit PRAC gene, fold-difference=10, P=3.48x10-57). In eQTL studies, rs3087967 genotype was associated with expression of 8 cis- and 21 trans-genes. Four of these (AKAP14, ADH5P4, ASGR2, RP11-342M1.7) showed differential effects by site, with strongest transeQTL signals in proximal colonic mucosa (e.g. AKAP14, beta=0.61, P=5.02x10-5) and opposite signals in distal mucosa (AKAP14, beta=-0.17, P=0.04). In summary, genetic variation at the chr11q23.1 risk locus imparts greater risk of distal rather than proximal CRC and exhibits site-specific differences in eQTL effects in normal mucosa.
Topographical differences in genomic control over gene expression relevant to CRC risk may underlie site-specific variation in CRC. Results may inform individualised CRC screening programmes.