Genome-Scale Discovery of DNA-Methylation Biomarkers for Blood-Based Detection of Colorectal Cancer

Abstract

BackgroundThere is an increasing demand for accurate biomarkers for early non-invasive colorectal cancer detection. We employed a genome-scale marker discovery method to identify and verify candidate DNA methylation biomarkers for blood-based detection of colorectal cancer.Methodology/Principal FindingsWe used DNA methylation data from 711 colorectal tumors, 53 matched adjacent-normal colonic tissue samples, 286 healthy blood samples and 4,201 tumor samples of 15 different cancer types. DNA methylation data were generated by the Illumina Infinium HumanMethylation27 and the HumanMethylation450 platforms, which determine the methylation status of 27,578 and 482,421 CpG sites respectively. We first performed a multistep marker selection to identify candidate markers with high methylation across all colorectal tumors while harboring low methylation in healthy samples and other cancer types. We then used pre-therapeutic plasma and serum samples from 107 colorectal cancer patients and 98 controls without colorectal cancer, confirmed by colonoscopy, to verify candidate markers. We selected two markers for further evaluation: methylated THBD (THBD-M) and methylated C9orf50 (C9orf50-M). When tested on clinical plasma and serum samples these markers outperformed carcinoembryonic antigen (CEA) serum measurement and resulted in a high sensitive and specific test performance for early colorectal cancer detection.Conclusions/SignificanceOur systematic marker discovery and verification study for blood-based DNA methylation markers resulted in two novel colorectal cancer biomarkers, THBD-M and C9orf50-M. THBD-M in particular showed promising performance in clinical samples, justifying its further optimization and clinical testing.

Recurrent patterns of DNA methylation in theZNF154,CASP8, andVHLpromoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

“…[13][14][15] Considerable effort has also been devoted to investigate mutational events that could explain cancer-related aberrant methylation through their effect on the epigenetic machinery. 16,17 Recently, the development of clinically relevant diagnostic tests for cancer based on methylation biomarkers measured in blood, urine, and other body fluids [18][19][20][21][22] have provided a glimpse into the biomedical applications that may become mainstream in the near future. 23 DNA methylation experiments performed by individual laboratories provide evidence for the identification of shared signatures of differential methylation that can separate tumors from normal controls.…”

Validation of a Real-Time PCR–Based Qualitative Assay for the Detection of Methylated SEPT9 DNA in Human Plasma

“…A number of methylation biomarkers have been found in circulating cell-free DNA (ccfDNA) in blood and are promising avenues to address this clinical need (10,(12)(13)(14)(15)(16)(17). Among those that have been rigorously studied, methylated SEPT9 6 (septin 9) is the most well characterized (18,19 ).…”

Accessing Genetic Information with Liquid Biopsies

“…However, there is definitive evidence suggesting the existence of epigenetic drivers, such as MLH1 CpG island promoter hypermethylation in colorectal cancer, which occur at high frequency and can stably propagate within cancer cells [45,48]. Accordingly, aberrant patterns of DNA methylation have been identified as cancer-specific biomarkers, and their clinical utility is actively being established [26,46,[49][50][51]. The most encouraging example is a multi-target stool DNA test developed by a company called Exact Science for colorectal cancer (CRC) early screening.…”

“…Targeted sequencing of specific CpG island promoter regions is the most clinically relevant because many cancer-associated promoter hypermethylation patterns have been identified and used as cancer biomarkers [46,[49][50][51]. For example, by analyzing a panel of 10 selected cancer hypermethylation markers through methylation-specific PCR on cfDNA, a sensitivity of 91% was reached among recurrent stage IV breast cancer patients [51].…”