title: Novel candidate colorectal cancer biomarkers identified by methylation microarray-based scanning.
abstract: DNA hypermethylation is a common epigenetic abnormality in colorectal cancers (CRCs) and a promising class of CRC screening biomarkers. We conducted a genome-wide search for novel neoplasia-specific hypermethylation events in the colon. We applied methylation microarray analysis to identify loci hypermethylated in 17 primary CRCs relative to eight non-neoplastic colonic mucosae (NCs) from neoplasia-free subjects. These CRC-associated hypermethylation events were then individually evaluated for their ability to discriminate neoplastic from non-neoplastic cases, based on real-time quantitative methylation-specific PCR (qMSP) assays in 113 colonic tissues: 51 CRCs, nine adenomas, 19 NCs from CRC patients (CRC-NCs), and 34 NCs from neoplasia-free subjects (control NCs). A strict microarray data filtering identified 169 candidate CRC-associated hypermethylation events. Fourteen of these 169 loci were evaluated using qMSP assays. Ten of these 14 methylation events significantly distinguished CRCs from age-matched control NCs (P<0.05 by receiver operator characteristic curve analysis); methylation of visual system homeobox 2 (VSX2) achieved the highest discriminative accuracy (83.3% sensitivity and 92.3% specificity, P<1×10(-6)), followed by BEN domain containing 4 (BEND4), neuronal pentraxin I (NPTX1), ALX homeobox 3 (ALX3), miR-34b, glucagon-like peptide 1 receptor (GLP1R), BTG4, homer homolog 2 (HOMER2), zinc finger protein 583 (ZNF583), and gap junction protein, gamma 1 (GJC1). Adenomas were significantly discriminated from control NCs by hypermethylation of VSX2, BEND4, NPTX1, miR-34b, GLP1R, and HOMER2 (P<0.05). CRC-NCs were significantly distinguished from control NCs by methylation of ALX3 (P<1×10(-4)). In conclusion, systematic methylome-wide analysis has identified ten novel methylation events in neoplastic and non-neoplastic colonic mucosae from CRC patients. These potential biomarkers significantly discriminate CRC patients from controls. Thus, they merit further evaluation in stool- and circulating DNA-based CRC detection studies.
authors.affiliation: Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, Maryland 21205, USA. ymori3@jhmi.edu
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Mori
authors.forename: Alexandru V
authors.initials: AV
authors.lastname: Olaru
authors.forename: Yulan
authors.initials: Y
authors.lastname: Cheng
authors.forename: Rachana
authors.initials: R
authors.lastname: Agarwal
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.forename: Delgermaa
authors.initials: D
authors.lastname: Luvsanjav
authors.forename: Wayne
authors.initials: W
authors.lastname: Yu
authors.forename: Florin M
authors.initials: FM
authors.lastname: Selaru
authors.forename: Susan
authors.initials: S
authors.lastname: Hutfless
authors.forename: Mark
authors.initials: M
authors.lastname: Lazarev
authors.forename: John H
authors.initials: JH
authors.lastname: Kwon
authors.forename: Steven R
authors.initials: SR
authors.lastname: Brant
authors.forename: Michael R
authors.initials: MR
authors.lastname: Marohn
authors.forename: David F
authors.initials: DF
authors.lastname: Hutcheon
authors.forename: Mark D
authors.initials: MD
authors.lastname: Duncan
authors.forename: Ajay
authors.initials: A
authors.lastname: Goel
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Meltzer
mesh_terms: D000236:Adenoma / Q000175:diagnosis / Q000235:genetics*; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D016022:Case-Control Studies; D003106:Colon / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000175:diagnosis / Q000235:genetics*; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000235:genetics; D057890:Epigenomics; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D012007:Rectum / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; D035683:MicroRNAs