Red meat intake interacts with a TGF-β-pathway-based polygenic risk score to impact colorectal cancer risk: Application of a novel approach for polygenic risk score construction
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Background
High intake of red and/or processed meat are established colorectal cancer (CRC) risk factors. Genome-wide association studies (GWAS) have reported 204 variants (G) associated with CRC risk. We used functional annotation data to identify subsets of variants within known pathways and constructed pathway-based Polygenic Risk Scores (pPRS) to model pPRS x environment (E) interactions.
Methods
A pooled sample of 30,812 cases and 40,504 CRC controls of European ancestry from 27 studies were analyzed. Quantiles for red and processed meat intake were constructed. The 204 GWAS variants were annotated to genes with AnnoQ and assessed for overrepresentation in PANTHER-reported pathways. pPRS’s were constructed from significantly overrepresented pathways. Covariate-adjusted logistic regression models evaluated pPRSxE interactions with red or processed meat intake in relation to CRC risk.
Results
A total of 30 variants were overrepresented in four pathways: Alzheimer disease-presenilin, Cadherin/WNT-signaling, Gonadotropin-releasing hormone receptor, and TGF- β signaling. We found a significant interaction between TGF- β -pPRS and red meat intake (p = 0.003). When variants in the TGF- β pathway were assessed, significant interactions with red meat for rs2337113 (intron SMAD7 gene, Chr18), and rs2208603 (intergenic region BMP5 , Chr6) (p = 0.013 & 0.011, respectively) were observed. We did not find evidence of pPRS x red meat interactions for other pathways or with processed meat.
Conclusions
This pathway-based interaction analysis revealed a significant interaction between variants in the TGF- β pathway and red meat consumption that impacts CRC risk.
Impact
These findings shed light into the possible mechanistic link between CRC risk and red meat consumption.
Impact statement
In this work, we developed pathway-based Polygenic Risk Scores, which for the first time suggested, that red meat intake interacts with variants overrepresented in TGF- β signaling pathway to increase colorectal cancer risk.
