Serum methylation of GALNT9, UPF3A, WARS, and LDB2 as non-invasive biomarkers for the early detection of colorectal cancer and premalignant adenomas

Abstract

Early detection has proven to be the most effective strategy to reduce the incidence and mortality of colorectal cancer (CRC). Nevertheless, most current screening programs suffer from low participation rates. A blood test may improve both the adherence to screening and the selection to colonoscopy. In this study, we conducted a serum-based discovery and validation of cfDNA methylation biomarkers for CRC screening in a multicentre cohort of 453 serum samples including healthy controls, benign pathologies, advanced adenomas (AA), and CRC. First, we performed an epigenome-wide methylation analysis with the MethylationEPIC array using a sample pooling approach, followed by a robust prioritization of candidate biomarkers for the detection of advanced neoplasia (AN: AA and CRC). Then, candidate biomarkers were validated by pyrosequencing in independent individual cfDNA samples. We report GALNT9, UPF3A, WARS, and LDB2 as new non-invasive biomarkers for the early detection of AN. The combination of GALNT9/UPF3A by logistic regression discriminated AN with 78.8% sensitivity and 100% specificity, outperforming the commonly used fecal immunochemical test and the methylated SEPT9 blood test. Overall, our results suggest that the combination methylated GALNT9/UPF3A has the potential to serve as a highly specific and sensitive blood-based test for screening and early detection of CRC.

Serum DNA methylome of the colorectal cancer serrated pathway

“…This dataset includes MethylationEPIC data of cfDNA pooled samples of NCF (n=3), non-advanced adenomas (n=5), advanced adenomas (n=10), and CRC (n=5). [24] None of the 330 DMPs from the serrated pathway was differentially methylated in samples from the conventional pathway (10% FDR). Unsupervised clustering and heatmap from Figure 3C shows no difference in the methylation levels of the 330 DMPs from the serrated pathway and no ability to group advanced neoplasia samples from the conventional pathway.…”

“…This dataset includes 23 cfDNA pooled samples grouped in NCF, non-advanced adenomas, advanced adenomas and CRC. [24] Serum differential methylation profiles were also tested in tissue samples from healthy colorectal mucosa (n=16) and serrated tumors (n=38) from the dataset GSE68060, [22] and from SSL (n=13) from the dataset E-MTAB-7854. [23] This analysis was limited to probes shared by the Methylation450k and MethyationEPIC BeadChip arrays.…”