Abstract
Using a bioinformatics-based strategy, we set out to identify hypermethylated genes that could serve as biomarkers for early detection of colorectal cancer (CRC) in stool. In addition, the complementary value to a Fecal Immunochemical Test (FIT) was evaluated. Candidate genes were selected by applying cluster alignment and computational analysis of promoter regions to microarray-expression data of colorectal adenomas and carcinomas. DNA methylation was measured by quantitative methylation-specific PCR on 34 normal colon mucosa, 71 advanced adenoma, and 64 CRC tissues. The performance as biomarker was tested in whole stool samples from in total 193 subjects, including 19 with advanced adenoma and 66 with CRC. For a large proportion of these series, methylation data for GATA4 and OSMR were available for comparison. The complementary value to FIT was measured in stool subsamples from 92 subjects including 44 with advanced adenoma or CRC. Phosphatase and Actin Regulator 3 (PHACTR3) was identified as a novel hypermethylated gene showing more than 70-fold increased DNA methylation levels in advanced neoplasia compared with normal colon mucosa. In a stool training set, PHACTR3 methylation showed a sensitivity of 55% (95% CI: 33-75) for CRC and a specificity of 95% (95% CI: 87-98). In a stool validation set, sensitivity reached 66% (95% CI: 50-79) for CRC and 32% (95% CI: 14-57) for advanced adenomas at a specificity of 100% (95% CI: 86-100). Adding PHACTR3 methylation to FIT increased sensitivity for CRC up to 15%. PHACTR3 is a new hypermethylated gene in CRC with a good performance in stool DNA testing and has complementary value to FIT.
Highlights
Screening for colorectal cancer (CRC) is the most efficient strategy for reducing death from this devastating disease
Stool-based DNA testing is an appealing approach for noninvasive early detection of CRC
We applied a bioinformatics approach for identifying novel hypermethylated genes in CRC. This resulted in the identification of Phosphatase and Actin Regulator 3 (PHACTR3) as a new hypermethylated gene in CRC, which showed to have complementary diagnostic power to Fecal Immunochemical Test (FIT) in a pilot series
Summary
Screening for colorectal cancer (CRC) is the most efficient strategy for reducing death from this devastating disease. 4–6) is widely used in screening programs in Europe and Japan, and is expected to reduce CRC mortality by around 30% [7] This test performance though, still leaves room for improvement which could come from molecular stool tests like those testing for tumor DNA in stool. The recently introduced combination of mutation markers with DNA methylation markers has yielded substantially improved test performance [13, 15, 16] Methylation markers on their own, either alone or combined, have yielded promising results, whereas the assays are technically less demanding [17,18,19,20,21,22,23]. Methylation markers are appealing for CRC screening even more because DNA methylation is an early event in colorectal development, preceding chromosomal abnormalities, and mutations [24]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
