Highly methylated genes in colorectal neoplasia: implications for screening.
Discriminant markers are required for accurate cancer screening. We evaluated genes frequently methylated in colorectal neoplasia to identify the most discriminant ones. Four genes specifically methylated in colorectal cancer [bone morphogenetic protein 3 (BMP3), EYA2, aristaless-like homeobox-4 (ALX4), and vimentin] were selected from 41 candidate genes and evaluated on 74 cancers, 62 adenomas, and 70 normal epithelia. Methylation status was analyzed qualitatively and quantitatively and confirmed by bisulfite genomic sequencing. Effect of methylation on gene expression was evaluated in five colon cancer cell lines. K-ras and BRAF mutations were detected by sequencing. Methylation of BMP3, EYA2, ALX4, or vimentin was detected respectively in 66%, 66%, 68%, and 72% of cancers; 74%, 48%, 89%, and 84% of adenomas; and 7%, 5%, 11%, and 11% of normal epithelia (P < 0.01, cancer or adenoma versus normal). Based on area under the curve analyses, discrimination was not significantly improved by combining markers. Comethylation was frequent (two genes or more in 72% of cancers and 84% of adenomas), associated with proximal neoplasm site (P < 0.001), and linked with both BRAF and K-ras mutations (P < 0.01). Cell line experiments supported silencing of expression by methylation in all four study genes. This study shows BMP3, EYA2, ALX4, and vimentin genes are methylated in most colorectal neoplasms but rarely in normal epithelia. Comethylation of these genes is common, and pursuit of complementary markers for methylation-negative neoplasms is a rational strategy to optimize screening sensitivity.
Zou
Hongzhi
H
Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
Harrington
Jonathan J
JJ
Shire
Abdirashid M
AM
Rego
Rafaela L
RL
Wang
Liang
L
Campbell
Megan E
ME
Oberg
Ann L
AL
Ahlquist
David A
DA
D000230:Adenocarcinoma / Q000235:genetics* / Q000517:prevention & control; D000236:Adenoma / Q000235:genetics; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D014408:Biomarkers, Tumor / Q000235:genetics*; D055398:Bone Morphogenetic Protein 3; D019485:Bone Morphogenetic Proteins / Q000235:genetics; D015179:Colorectal Neoplasms / Q000235:genetics* / Q000517:prevention & control; D019175:DNA Methylation; D017931:DNA Primers; D004273:DNA, Neoplasm / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D008297:Male; D008403:Mass Screening / Q000379:methods*; D008875:Middle Aged; D009154:Mutation; D009687:Nuclear Proteins / Q000235:genetics; D017027:Protein Tyrosine Phosphatases / Q000235:genetics; D011518:Proto-Oncogene Proteins / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D012372:ROC Curve; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D014157:Transcription Factors / Q000235:genetics; D014746:Vimentin / Q000235:genetics; D018631:ras Proteins / Q000235:genetics
C416676:ALX4 protein, human; C525757:BMP3 protein, human; D014408:Biomarkers, Tumor; D055398:Bone Morphogenetic Protein 3; D019485:Bone Morphogenetic Proteins; D017931:DNA Primers; D004273:DNA, Neoplasm; D004268:DNA-Binding Proteins; D047908:Intracellular Signaling Peptides and Proteins; C117307:KRAS protein, human; D009687:Nuclear Proteins; D011518:Proto-Oncogene Proteins; D014157:Transcription Factors; D014746:Vimentin; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; C106938:EYA2 protein, human; D017027:Protein Tyrosine Phosphatases; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins