Pro-inflammatory cytokine polymorphisms in ONECUT2 and HNF4A and primary colorectal carcinoma: a post genome-wide gene-lifestyle interaction study

Abstract

Immune-related molecular and genetic pathways that are connected to colorectal cancer (CRC) and lifestyles in postmenopausal women are incompletely characterized. In this study, we examined the role of pro-inflammatory biomarkers such as C-reactive protein (CRP) and interleukin-6 (IL-6) in those pathways. Through selection of the best predictive single-nucleotide polymorphisms (SNPs) and lifestyles, our goal was to improve the prediction accuracy and ability for CRC risk. Using large cohort data of postmenopausal women from the Women's Health Initiative Database for Genotypes and Phenotypes Study, we previously conducted a genome-wide association (GWA) for a CRP and IL-6 gene-behavioral interaction study. For the present study, we added GWA-SNPs from outside GWA studies, resulting in a total of 152 SNPs. Together with 41 selected lifestyles, we performed a 2-stage multimodal random survival forest analysis with generalized multifactor dimensionality reduction approach to construct CRC risk profiles. Overall and in obesity strata (by body mass index, waist circumference, waist-to-hip ratio, exercise, and dietary fat intake), we identified the best predictive genetic markers in inflammatory cytokines and lifestyles. Across the strata, 2 SNPs (ONECUT2 rs4092465 and HNF4A rs1800961) and 1 lifestyle factor (relatively short-term past use of oral contraceptives) were the most common and strongest predictive markers for CRC risk. The risk profile that combined those variables exhibited synergistically increased risk for CRC; this pattern appeared more strongly in obese and inactive subgroups. Our results may contribute to improved predictability for CRC and suggest genetically targeted lifestyle interventions for women carrying the inflammatory-risk genotypes, reducing CRC risk.

Keywords: C-reactive protein; Random survival forest; colorectal cancer; endogenous estrogen; generalized multifactor dimensionality reduction; inflammatory cytokines; interleukin-6; obesity; oral contraceptive; postmenopausal women.

Figure 1

Two-stage random survival forest (RSF) and generalized multifactor dimensionality reduction (GMDR). (BMI, body mass index; CRC, colorectal cancer; GWA, genome-wide association; MD, minimal depth; SNP, single-nucleotide polymorphism; WHR, waist-to-hip ratio; WST, waist circumference; VIMP, variable of importance. * WHR subgroups combined 2 our GWA and 65 outside GWA SNPs).

Figure 2

Overall analysis: the second stage of random survival forest (RSF) analysis with 18 single-nucleotide polymorphisms and 12 behavioral factors selected from the first stage of RSF. A. Comparison of minimal depth and VIMP rankings. (BMI, body mass index; E+P, exogenous estrogen + progestin; VIMP, variable of importance. Note: The 3 variables within the gold ellipse were identified as the most influential predictors. B. Out-of-bag concordance index (C-index). (Improvement in the out-of-bag C-index was observed when the top 3 variables [●] were added to the model, whereas other variables [○] did not further improve the accuracy of prediction).

Figure 3

Cumulative colorectal cancer incidence rate for the 4 most influential variables (3 SNPs and 1 behavioral factor) based on random survival forest analyses. (SNPs, single-nucleotide polymorphisms. Dashed red lines indicate 95% confidence intervals).

Figure 4

Forest plot of the combined (A) and joint (B) effect of past OC use and risk genotypes on CRC risk overall and in MET subgroups. Plot (A) shows the independent and combined effect of risk genotypes and OC use on CRC risk, and Plot (B) shows the joint tests for risk genotypes with OC use, presented as the 95% CIs (indicated with red lines) and the estimates (proportional to the size of the blue squares). The analyzed risk genotypes included ONECUT2 rs4092465 GA and HNF4A rs1800961 TT. (CI, confidence interval; CRC, colorectal cancer; HR, hazard ratio; MET, metabolic equivalent; OC, oral contraceptive).