Abstract A30: DNA methylation field defects in colorectal cancer patients.
Authors: Li Ling , Cheng Yulan , Ibrahim Saliat , Meltzer Stephen , Mori Yuriko 
Published: January 2014

Background: Colorectal cancer (CRC)-associated epigenetic abnormalities can develop in pre-neoplastic stages (“epigenetic field defect”) and are detectable throughout the colorectal mucosae as well as in colonic epithelial cells shed into stools. Thus, epigenetic field defects may be useful biomarkers in early detection and risk prediction of CRC in subjects without colonoscopically detectable abnormalities. We carried out a genome-wide analysis of DNA methylation field defects in CRC patients.

Methods: Morphologically normal colonic tissues were subjected to the genome-wide DNA methylation microarray analysis. The analyzed tissues consisted of 6 colonic tissues from CRC cases (61-77 years of age; herein referred to as CRC_NCs) and 18 colonic tissues from control subjects (22-85 years of age) with no history of colorectal neoplasias. In assessing DNA methylation field defect, we used 9 of the 18 control tissues that were age-, gender-, and anatomical site-matched to the CRC_NCs as the matched controls (61-77 years of age). The array platform that was employed in this study measured DNA methylation using bisulfite converted sequence-specific probes and is capable of interrogating more than 480,000 individual CpG loci.

Results: Principal component analysis of the microarray data revealed that age was the strongest contributing factor to the genome-wide DNA methylation variability in morphologically normal colonic tissues (corresponding to 64.6% of total variability, adjusted p-value&lt;0.05). Anatomical site, followed by presence of concurrent CRC, demonstrated a significant but minor contribution.

Relative to the matched controls, 8,454 (1.8%) of the tested autosomal loci were significantly differentially methylated in CRC_NCs (cutoff: Student t-test p&lt;0.05 and delta beta&gt;0.05). In these 8,454 loci, correlation coefficient between age and methylation was significantly but inversely associated with the T–values for differential methylation in CRC_NC (R=-0.63, p&lt;1E-308). Of the 8,454 loci, 212 loci were designated as the candidate field defect biomarkers for CRC_NC detection based on the absence of aging- or anatomical site-dependent methylation.

Pilot real-time quantitative methylation specific PCR analyses were performed on four hypermethylation field defect biomarker candidates using an expanded colonic tissue cohort consisting of 29 CRC_NCs and 27 matched controls. Significant or trend toward hypermethylation in CRC_NCs relative to matched controls were observed in all four tested candidates. Two candidates significantly discriminated CRC_NCs from matched controls according to the Receiver-operating characteristics curve analysis (AUC 0.77 and 0.78, p=1E-4).

Conclusions: Genome-wide DNA methylation signature in morphologically normal colonic tissue is primarily defined by age, rather than presence of concurrent CRC. A large fraction of methylation field defects are suppression of aging-associated DNA methylation changes, suggesting a protective role of aging-associated DNA methylation changes against early stage carcinogenesis. A pilot quantitative PCR-based assessment in an expanded tissue cohort indicate that the methylation field defects detected by the current microarray analysis include promising candidate biomarkers for early detection of CRC patients and cases at a higher risk of developing CRC.

Citation Format: Ling Li, Yulan Cheng, Saliat Ibrahim, Stephen Meltzer, Yuriko Mori. DNA methylation field defects in colorectal cancer patients. [abstract]. In: Proceedings of the Eleventh Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2012 Oct 16-19; Anaheim, CA. Philadelphia (PA): AACR; Cancer Prev Res 2012;5(11 Suppl):Abstract nr A30.

Note: This abstract was not presented at the conference.