title: Identification of novel DNA methylation markers in colorectal cancer             using MIRA-based microarrays.
abstract: To identify novel hypermethylated genes in colorectal cancer (CRC) and to             test their potential application in CRC early diagnosis, a genome-wide screening             of 57,723 CpG dinucleotides covering 4,010 genes was performed using MIRA-based             microarrays in paired DNA samples extracted from 3 fresh frozen CRC tissues and             their matching non-cancer tissues from 3 CRC patients undergoing curative surgery.             Candidate hypermethylated genes screened by MIRA-based microarrays were further             validated in independent CRC samples. A total of 297 CpG dinucleotides covering             211 genes were found to be hypermethylated in CRC tissues. From these 211 candidate             methylated genes, three novel hypermethylated genes with more than four probes             positive were picked up for validation. Direct bisulfite sequencing revealed that             methylations occurred at multiple CpG sites of these three genes in cancer tissues,             especially for PHOX2B and FGF12. Combined bisulfite restriction analysis showed             that these three genes were methylated in cancer samples but not in non-cancer             samples. We also compared the methylation levels of these three novel hypermethylated             genes with those of vimentin and SEPT9, well-known hypermethylated genes in CRC,             and found that methylated PHOX2B, FGF12 and GAD2 were better than methylated vimentin             and SEPT9 in differentiating CRC cancer tissue from non-cancer tissue. Significant             enrichment analysis of GO terms of the hypermethylated genes showed that a high             proportion of hypermethylated genes in cancer tissues are involved in the regulation             of transcription. In conclusion, we found a set of novel hypermethylated genes             in CRC, which may have potential to be used as biomarkers for the early diagnosis             of CRC.
authors.affiliation: Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, PR China.
authors.forename: Hai
authors.initials: H
authors.lastname: Li
authors.forename: Yong
authors.initials: Y
authors.lastname: Du
authors.forename: Dong
authors.initials: D
authors.lastname: Zhang
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Wang
authors.forename: Chun
authors.initials: C
authors.lastname: Yang
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Wei-Jie
authors.initials: WJ
authors.lastname: Wang
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.forename: Wei-Guo
authors.initials: WG
authors.lastname: Hong
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.forename: Yin-Xue
authors.initials: YX
authors.lastname: Yang
mesh_terms: D001483:Base Sequence; D014408:Biomarkers, Tumor / Q000235:genetics*; D016000:Cluster Analysis; D015179:Colorectal Neoplasms / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D005346:Fibroblast Growth Factors / Q000235:genetics*; D005968:Glutamate Decarboxylase / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D058112:Septins / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*; D014746:Vimentin / Q000235:genetics
chemical_list: D014408:Biomarkers, Tumor; C486356:FGF12 protein, human; D018398:Homeodomain Proteins; C109220:NBPhox protein; D014157:Transcription Factors; D014746:Vimentin; D005346:Fibroblast Growth Factors; C474315:SEPTIN9 protein, human; D058112:Septins; D005968:Glutamate Decarboxylase; C401141:glutamate decarboxylase 2