Validation of Methylation Biomarkers that Distinguish Normal Colon Mucosa of Cancer Patients from Normal Colon Mucosa of Patients without Cancer

Abstract

We have validated differences in DNA methylation levels of candidate genes previously reported to discriminate between normal colon mucosa of colon cancer patients and normal colon mucosa of individuals without cancer. Here, we report that CpG sites in 16 of the 30 candidate genes selected show significant differences in mean methylation level in normal colon mucosa of 24 cancer patients and 24 controls. A support vector machine trained on these data and data for an additional 66 CpGs yielded an 18-gene signature, composed of 10 of the validated candidate genes plus eight additional candidates. This model exhibited 96% sensitivity and 100% specificity in a 40-sample training set and classified all eight samples in the test set correctly. Moreover, we found a moderate-strong correlation (Pearson coefficients r=0.253-0.722) between methylation levels in colon mucosa and methylation levels in peripheral blood for seven of the 18 genes in the support vector model. These seven genes, alone, classified 44 of the 48 patients in the validation set correctly and five CpGs selected from only two of the seven genes classified 41 of the 48 patients in the discovery set correctly. These results suggest that methylation biomarkers may be developed that will, at minimum, serve as useful objective and quantitative diagnostic complements to colonoscopy as a cancer-screening tool. These data also suggest that it may be possible to monitor biomarker methylation levels in tissues collected much less invasively than by colonoscopy.

DNA methylation differences between in vitro- and in vivo-conceived children are associated with ART procedures rather than infertility

“…The significant results of ANOVA were analyzed using Tukey’s HSD test. One-tailed t -tests were used in comparing mean methylation levels between infertile ART and fertile control groups for the validation of our previous array findings [ 1 , 30 ] as we had a prior expectation for the direction of change and the use of one-sided tests is an accepted statistical procedure in validation studies [ 63 ]. Two-tailed t -tests were used for comparing fertile control and donor oocyte ART groups.…”

RW‐2018—Research Workshop: The Effect of Nutrition on Epigenetic Status, Growth, and Health

“…Populations being studied using this approach include children exposed to unusual environments early in development (children conceived by assisted reproduction), 22,23 children who are small for gestational age/have a low birth weight, and individuals with colorectal cancer because of the well-documented association between this disease and high-fat diets. 33,34 DNAm differences associated with both assisted reproduction and low birth weight have been found and validated in independent populations. However, the magnitude of these differences is small in comparison to populationlevel variability.…”

“…Thus, DNAm can serve as a potential marker of undesirable environmental exposures by examining normal tissues in individuals subjected to such an exposure. Populations being studied using this approach include children exposed to unusual environments early in development (children conceived by assisted reproduction), children who are small for gestational age/have a low birth weight, and individuals with colorectal cancer because of the well‐documented association between this disease and high‐fat diets …”

Aberrant expression of MYD88 via RNA‐controlling CNOT4 and EXOSC3 in colonic mucosa impacts generation of colonic cancer

“…Genetic and epigenetic changes play critical roles in the onset and development of CRC, and several papers have reported that it may be valuable to use quantitative objective measures of epigenetic changes in normal tissues to detect CRC or precancerous lesions. 34 , 35 , 36 , 37 , 38 , 39 Although comparisons of DNA methylation status in the normal colonic mucosa of patients with or without colonic cancer have been reported, 34 this method seems to be inadequate in the clinic.…”