Genome-wide interaction analysis of folate for colorectal cancer risk

Abstract

Background: Epidemiological and experimental evidence suggests that higher folate intake is associated with decreased colorectal cancer (CRC) risk; however, the mechanisms underlying this relationship are not fully understood. Genetic variation that may have a direct or indirect impact on folate metabolism can provide insights into folate's role in CRC.

Objectives: Our aim was to perform a genome-wide interaction analysis to identify genetic variants that may modify the association of folate on CRC risk.

Methods: We applied traditional case-control logistic regression, joint 3-degree of freedom, and a 2-step weighted hypothesis approach to test the interactions of common variants (allele frequency >1%) across the genome and dietary folate, folic acid supplement use, and total folate in relation to risk of CRC in 30,550 cases and 42,336 controls from 51 studies from 3 genetic consortia (CCFR, CORECT, GECCO).

Results: Inverse associations of dietary, total folate, and folic acid supplement with CRC were found (odds ratio [OR]: 0.93; 95% confidence interval [CI]: 0.90, 0.96; and 0.91; 95% CI: 0.89, 0.94 per quartile higher intake, and 0.82 (95% CI: 0.78, 0.88) for users compared with nonusers, respectively). Interactions (P-interaction < 5×10^-8) of folic acid supplement and variants in the 3p25.2 locus (in the region of Synapsin II [SYN2]/tissue inhibitor of metalloproteinase 4 [TIMP4]) were found using traditional interaction analysis, with variant rs150924902 (located upstream to SYN2) showing the strongest interaction. In stratified analyses by rs150924902 genotypes, folate supplementation was associated with decreased CRC risk among those carrying the TT genotype (OR: 0.82; 95% CI: 0.79, 0.86) but increased CRC risk among those carrying the TA genotype (OR: 1.63; 95% CI: 1.29, 2.05), suggesting a qualitative interaction (P-interaction = 1.4×10^-8). No interactions were observed for dietary and total folate.

Conclusions: Variation in 3p25.2 locus may modify the association of folate supplement with CRC risk. Experimental studies and studies incorporating other relevant omics data are warranted to validate this finding.

Keywords: CRC; European; GWIS; SYN2; TIMP4; colorectal cancer; folate; folic acid; genome-wide; interaction; synapsin; tissue inhibitor of metalloproteinase 4.

FIGURE 1

Summary of the random-effects meta-analysis results on the association between folate intake and colorectal cancer risk. CRC, colorectal cancer; I², inconsistency index.

FIGURE 2

Functional annotation and locus zoom plots of the 2 loci that interacted with folic acid supplement to alter risk of colorectal cancer: (A) variant chr3:12041456 (rs150924902); (B) variant chr6:23445253 (rs1291413). The Manhattan plots (left) provide an overview of the genome-wide interaction scan (GWIS) results, and the locus zoom plots (middle) display regional information centered around the top GWIS findings. The functional annotation plot (right) shows how the top findings per locus colocalize to transcriptionally active regions (peaks), using different markers of chromatin accessibility (ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing; DHS, DNase I hypersensitive sites; H3K27ac, acetylation of the lysine residue at N-terminal position 27 of the histone H3 protein; H3K4me1, mono-methylation at the 4th lysine residue of the histone H3 protein), and information from genetically diverse human CRC specimens. SYN2, Synapsin II; TAMM41, TAM41 mitochondrial translocator assembly and maintenance homolog; TIMP4, tissue inhibitor of metalloproteinase 4.