Genome-wide association studies and Mendelian randomization analyses provide insights into the causes of early-onset colorectal cancer

Abstract

Background: The incidence of early-onset colorectal cancer (EOCRC; diagnosed <50 years of age) is rising globally; however, the causes underlying this trend are largely unknown. CRC has strong genetic and environmental determinants, yet common genetic variants and causal modifiable risk factors underlying EOCRC are unknown. We conducted the first EOCRC-specific genome-wide association study (GWAS) and Mendelian randomization (MR) analyses to explore germline genetic and causal modifiable risk factors associated with EOCRC.

Patients and methods: We conducted a GWAS meta-analysis of 6176 EOCRC cases and 65 829 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), the Colorectal Transdisciplinary Study (CORECT), the Colon Cancer Family Registry (CCFR), and the UK Biobank. We then used the EOCRC GWAS to investigate 28 modifiable risk factors using two-sample MR.

Results: We found two novel risk loci for EOCRC at 1p34.1 and 4p15.33, which were not previously associated with CRC risk. We identified a deleterious coding variant (rs36053993, G396D) at polyposis-associated DNA repair gene MUTYH (odds ratio 1.80, 95% confidence interval 1.47-2.22) but show that most of the common genetic susceptibility was from noncoding signals enriched in epigenetic markers present in gastrointestinal tract cells. We identified new EOCRC-susceptibility genes, and in addition to pathways such as transforming growth factor (TGF) β, suppressor of Mothers Against Decapentaplegic (SMAD), bone morphogenetic protein (BMP) and phosphatidylinositol kinase (PI3K) signaling, our study highlights a role for insulin signaling and immune/infection-related pathways in EOCRC. In our MR analyses, we found novel evidence of probable causal associations for higher levels of body size and metabolic factors-such as body fat percentage, waist circumference, waist-to-hip ratio, basal metabolic rate, and fasting insulin-higher alcohol drinking, and lower education attainment with increased EOCRC risk.

Conclusions: Our novel findings indicate inherited susceptibility to EOCRC and suggest modifiable lifestyle and metabolic targets that could also be used to risk-stratify individuals for personalized screening strategies or other interventions.

Keywords: GWAS; Mendelian randomization; early-onset colorectal cancer; genetics; risk factors.

Figure 1

Study design of the early-onset colorectal cancer (EOCRC) genome-wide association study (GWAS) and Mendelian randomization (MR) analyses. 25(OH)D, 25-hydroxyvitamin D; 2hGlucose, 2-hour glucose; BMI, body mass index; BMR, basal metabolic rate; eQTL, expression quantitative trait locus; HbA_1c, glycated hemoglobin; IGF1, insulin-like growth factor 1; IGFBP3, insulin-like growth factor-binding protein 3; IVW, inverse variance-weighted; PRESSO, pleiotropy residual sum and outlier; SNP, single-nucleotide polymorphism; systolic BP, systolic blood pressure; WC, waist circumference; WHR, waist-to-hip ratio.

Figure 2

Early-onset colorectal cancer (EOCRC) genome-wide results. (A) Manhattan plots displaying the two new and 10 known genome-wide associations between common and rare minor allele frequency > 0.5%, germline genetic variants and EOCRC. The y-axis represents the –log10 values of the meta-analysis P-values. (B) Partitioned heritability enrichment estimates for the 28 functional annotations conducted in linkage disequilibrium score regression. (C) Cell-type-specific heritability estimates of EOCRC across different histone marks. CNS, central nervous system; SNP, single-nucleotide polymorphism.

Figure 3

Regional plots of the two new early-onset colorectal cancer risk loci. The genome-wide association study meta-analysis −log10 P-values (y-axis) of the single-nucleotide polymorphisms (SNPs) are shown according to their chromosomal positions (x-axis) based on GRCh37 in the main panel. The extent of linkage disequilibrium with the top SNP is denoted by the color scheme from gray (r² < 0.1) to dark red (r² = 1.0), with r² estimated from EUR 1000 Genomes data. The lower panel shows the 15-core chromatin states from the Roadmap Epigenomics project (E075, colonic mucosa; E076, colon smooth muscle; E106, sigmoid colon; E101, rectal mucosa 1; E102, rectal mucosa 2; E103, rectal smooth muscle; E084, fetal large intestine). The lowermost panel shows the –log10 P-values from the expression quantitative trait locus (eQTL) analysis where available. The semicircular plot on the right shows Hi-C chromatin interaction involving the credible SNP set in the loci from the GM12878 cell line. The genes in green represent eQTL-mapped genes, black represents chromatin interaction-mapped, and red are both eQTL and chromatin interaction-mapped genes at each locus.

Figure 4

Summary of prioritized candidate genes associated with early-onset colorectal cancer risk. Shown are the 44 candidate genes identified in this study and gene-level functional annotation from the Gene Ontology database and literature search. Genes in burgundy are the genes identified in the two newly identified loci; gene names in black are previously prioritized genes in known loci, and green-cyan genes are the newly identified genes in known risk loci. Red blocks in front of gene names represent genes with nonsynonymous coding variants, dark green bars represents positional mapping; dark magenta bars represent chromatin-interaction; dark blue bars represents protein-protein interaction hubs, and light green bars represents eQTL mapping. Akt, protein kinase B; BMP, bone morphogenetic protein; eQTL, expression quantitative trait loci; PI3K, phosphatidylinositol kinase; PPI, protein–protein interaction; TGF, transforming growth factor.

Figure 5

Mendelian randomization (MR) analyses. Odds ratios (ORs) from inverse variance-weighted MR analysis for the association between putative risk factors and early-onset colorectal cancer (EOCRC). All associations are expressed as OR per standard deviation (SD) increase in the risk factor except for alcoholic drinks per week and fasting insulin, which were expressed as OR per unit increase in the natural logarithm of the exposures. For categorical risk factors such as smoking initiation (ever versus never), type 2 diabetes (yes versus no), and physical activity (inactive versus active), the ORs were expressed as unit change in the exposure, compared with the reference group. 25(OH)D, 25-hydroxyvitamin D; HbA_1c, glycated hemoglobin; IGF, insulin growth factor; MVPA, moderate-to-vigorous physical activity; SNP, single-nucleotide polymorphism.