Identification and Validation of Colorectal Neoplasia–Specific Methylation Markers for Accurate Classification of Disease

• Published in: Molecular cancer research Vol. 5; no. 2; pp. 153 - 163
• Main Authors: Model, Fabian, Osborn, Neal, Ahlquist, David, Gruetzmann, Robert, Molnar, Bela, Sipos, Ferenc, Galamb, Orsolya, Pilarsky, Christian, Saeger, Hans-Detlev, Tulassay, Zsolt, Hale, Kari, Mooney, Suzanne, Lograsso, Joseph, Adorjan, Peter, Lesche, Ralf, Dessauer, Andreas, Kleiber, Joerg, Porstmann, Baerbel, Sledziewski, Andrew, Lofton-Day, Catherine
• Format: Journal Article
• Language: English
• Published: United States American Association for Cancer Research 01-02-2007
• Subjects: Biomarkers, Tumor - analysis; Cluster Analysis; colorectal cancer; Colorectal Neoplasms - classification; Colorectal Neoplasms - metabolism; DNA; DNA Methylation; DNA, Neoplasm - metabolism; Humans; methylation; microarray; molecular biomarkers; neoplasia; Oligonucleotide Array Sequence Analysis - methods; Polymerase Chain Reaction
• ISSN: 1541-7786; 1557-3125
• DOI: 10.1158/1541-7786.MCR-06-0034

Aberrant DNA methylation occurs early in oncogenesis, is stable, and can be assayed in tissues and body fluids. Therefore,
genes with aberrant methylation can provide clues for understanding tumor pathways and are attractive candidates for detection
of early neoplastic events. Identification of sequences that optimally discriminate cancer from other diseased and healthy
tissues is needed to advance both approaches. Using well-characterized specimens, genome-wide methylation techniques were
used to identify candidate markers specific for colorectal neoplasia. To further validate 30 of these candidates from genome-wide
analysis and 13 literature-derived genes, including genes involved in cancer and others with unknown functions, a high-throughput
methylation-specific oligonucleotide microarray was used. The arrays were probed with bisulfite-converted DNA from 89 colorectal
adenocarcinomas, 55 colorectal polyps, 31 inflammatory bowel disease, 115 extracolonic cancers, and 67 healthy tissues. The
20 most discriminating markers were highly methylated in colorectal neoplasia (area under the receiver operating characteristic
curve > 0.8; P < 0.0001). Normal epithelium and extracolonic cancers revealed significantly lower methylation. Real-time PCR assays developed
for 11 markers were tested on an independent set of 149 samples from colorectal adenocarcinomas, other diseases, and healthy
tissues. Microarray results could be reproduced for 10 of 11 marker assays, including eight of the most discriminating markers
(area under the receiver operating characteristic curve > 0.72; P < 0.009). The markers with high specificity for colorectal cancer have potential as blood-based screening markers whereas
markers that are specific for multiple cancers could potentially be used as prognostic indicators, as biomarkers for therapeutic
response monitoring or other diagnostic applications, compelling further investigation into their use in clinical testing
and overall roles in tumorigenesis. (Mol Cancer Res 2007;5(2):153–63)