Abstract A09: The relationship between DNA methylation in one-carbon metabolism genes and colorectal adenoma risk
Authors: Ho Vikki , Ashbury Janet A. , Taylor Sherryl , Vanner Stephen , King Will D. 
Published: October 2015

Background: The one-carbon (1C) metabolism cycle consists of a network of interrelated biochemical reactions that provide 1C units required for critical intracellular processes. Polymorphisms in MTHFR and DMNT3b, genes central to the 1C metabolism cycle, and colorectal cancer risk have been reported. Variation in the expression of genes may be attributable to functional polymorphisms; but, it is increasingly clear that epigenetic variation also affects gene expression. DNA methylation, which involves the covalent addition of a methyl group to cytosine residues that precede guanine (CpG), is the most commonly studied epigenetic mechanism. This research investigated the relationship between DNA methylation in the MTHFR and DNMT3b genes, and colorectal adenoma risk; higher methylation was hypothesized to decrease gene expression and contribute to colorectal adenoma risk.

Methods: A cross-sectional study recruited 272 patients aged 40-65 undergoing a screening colonoscopy. DNA methylation in the MTHFR and DNMT3b genes was quantified in DNA isolated from blood leukocytes using the Sequenom EpiTYPER® technology. Genomic regions of interest of each gene were selected based on location of CpG islands (1000-2000 base pairs) around the transcriptional start site.

Raw data consisted of methylation ratios for 53 and 82 CpG units (a unit consists of either an individual CpG site or aggregates of multiple CpG sites) for MTHFR and DNMT3b, respectively; methylation ratio equals the percentage of methylated cytosines at a specific CpG unit of a gene, divided by the total number of copies of that CpG unit in the sample. Methylation data was cleaned to remove CpG units with potentially unreliable methylation ratios and those with little variability (SD&lt;0.02). After data cleaning, a total of 14 MTHFR and 43 DNMT3b CpG units remained. For CpG units with missing values, the mean of each unit was assigned (occurred &lt;11.4% of units); only participants with data for greater than 90% of the CpG units were included in this study yielding a total of 260 participants.

Logistic regression was used to examine relationships between DNA methylation in MTHFR and DNMT3b on colorectal adenoma risk in separate sex- and age-adjusted models. Gene-specific DNA methylation for MTHFR and DNMT3b was conceptualized using two approaches: 1) a composite measure representing average methylation across all CpG units and; 2) unsupervised principal component (PC) analysis, a pattern derivation and data-reduction approach, to develop a smaller number of PCs which account for most of the variance in the methylation of CpG units. Composite and PC measures were categorized using equal-distant cut-points.

Results: In our study population of 86 patients with colorectal adenoma and 174 patients with normal colonoscopies, no associations were observed between overall average DNA methylation in MTHFR or DNMT3b, and colorectal adenoma risk. Using unsupervised PC analysis, 3 PCs were derived accounting for 42% and 54% of the variance in the CpG units of MTHFR and DNMT3b, respectively. No association was observed in PC analysis for MTHFR. For DNMT3b, a higher score in PC1 was associated with colorectal adenoma risk (p=0.02); specifically, CpG units approximately 250 base pairs 5' and 3' of the transcriptional start site were found to load heavily onto PC1and higher methylation in this region was found to be associated with colorectal adenoma risk (OR=4.01 (95% CI: 1.17-13.78) when contrasting the highest versus lowest category of methylation).

Conclusion: DNMT3b plays an important role in establishing and maintaining methylation patterns. Results of this novel investigation of epigenetic changes in 1C metabolism genes and colorectal adenoma risk suggest that alterations in methylation of the DNMT3b gene may be relevant to colorectal cancer etiology.

Citation Format: Vikki Ho, Janet A. Ashbury, Sherryl Taylor, Stephen Vanner, Will D. King. The relationship between DNA methylation in one-carbon metabolism genes and colorectal adenoma risk. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr A09.