Investigating the role of ALDH3B2 and FUT2 as potential risk genes to colorectal cancer through computational analysis and gene expression study of colonic cells, and utilizing colorectal cancer cell lines to explore gene-environment interactions

Abstract

The rise of genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) has brought to light numerous genetic loci known or predicted to be involved in conferring risk to various cancers. Using a systems genetics approach of GWAS and TWAS, this study sought to investigate two identified genes, ALDH3B2 and FUT2, in order to better understand their potential contributions to colorectal cancer (CRC) risk.

ALDH3B2, of the evolutionarily-conserved aldehyde dehydrogenase gene superfamily, is theorized to encode an enzyme that catalyzes the oxidation of toxic fatty aldehydes to their corresponding carboxylic acids. Attempts to isolate this gene in the transcriptome of three CRC cell lines—HCT116, HT29, and DLD1—using traditional PCR methodology consistently yielded no product despite the positive control of wild-type mouse cDNA being successfully amplified. This lack of evidence for a transcriptional product for ALDH3B2 supports previous findings that human ALDH3B2 is likely an un-transcribed pseudogene with no enzymatic functionality.

FUT2 encodes a fucosyltransferase that is central to the biochemical pathway responsible for the expression of the A and B antigens in non-blood bodily fluids. At least three transcript forms of FUT2 were identified in CRC cell lines. Differences in allele-specific expression of the well-documented functional nonsense mutation rs601338 were investigated in DLD1 cells, which were confirmed bioinformatically to be heterozygous at the nonsense rs601338 SNP. Furthermore, FUT2 has a known association with vitamin B12 levels. To probe the presence of a potential gene-environment interaction between FUT2 expression and vitamin B12, DLD1 cultures were treated with supplemental vitamin B12. Changes in FUT2 gene expression of the different transcripts were analyzed by RT-qPCR with mixed results, suggesting that further investigation is needed into this potential gene-environment interaction. By exploring the complex interplay between genetic variation and environmental factors, we aim to further clarify strategies for colorectal cancer prevention and control.