Genome-Wide Identification and Validation of a Novel Methylation Biomarker, SDC2, for Blood-Based Detection of Colorectal Cancer TaeJeong Oh, Nayoung.

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Presentation transcript:

Genome-Wide Identification and Validation of a Novel Methylation Biomarker, SDC2, for Blood-Based Detection of Colorectal Cancer TaeJeong Oh, Nayoung Kim, Youngho Moon, Myung Soon Kim, Benjamin D. Hoehn, Chan Hee Park, Tae Soo Kim, Nam Kyu Kim, Hyun Cheol Chung, Sungwhan An The Journal of Molecular Diagnostics Volume 15, Issue 4, Pages 498-507 (July 2013) DOI: 10.1016/j.jmoldx.2013.03.004 Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Stepwise filtering processes for candidate gene selection. The methylated DNA was separately enriched from 12 primary colorectal tumors (T) and paired, adjacent nontumor tissues (NT) by a MeDIA technique. The methylated DNAs (Cy5) were individually compared with amplified common reference DNA (Cy3) without methylation enrichment. The 43,097 reliable probes were selected and unsupervised clustering was performed based on Pearson's correlation. The heat map shows the methylation status of the statistically significant 32 hypermethylated and 41 hypomethylated genes. Six novel candidate genes hypermethylated in primary colorectal tumors were finally selected. The Journal of Molecular Diagnostics 2013 15, 498-507DOI: (10.1016/j.jmoldx.2013.03.004) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Quantitative bisulfite pyrosequencing assay of six candidate genes in cell lines and normal tissues from healthy individuals. The methylation levels were calculated for all examined CpGs in target regions. A: MtI values for each gene were plotted with results from pyrosequencing in two CRC cell lines, Caco-2 and HCT116. B: The methylation levels of the six genes were plotted in healthy normal tissues from an 83-year-old woman and a 24-year-old man. C: Methylation status of three of the genes was evaluated in primary tumors (T) and paired, adjacent nontumor tissues (NT) from 12 CRC patients from the initial CpG microarray analysis. MtI values were plotted from pyrosequencing results. Samples from the same patient are linked with a straight line. ∗P = 0.0011; †P < 0.0001, Paired t-test. The Journal of Molecular Diagnostics 2013 15, 498-507DOI: (10.1016/j.jmoldx.2013.03.004) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Refinement of the best methylation target and clinical verification of SDC2 in match-paired colorectal tissues from CRC patients. A: Three pyrosequencing target regions were designed for CpG islands of the SDC2 gene: R1 for promoter and R2 and R3 for the 5′ UTR. The transcription start site (TSS), 5′ UTR, and coding sequence (CDS) are indicated as such, and the three bisulfite-PCR target regions are indicated by horizontal bars. B: MtI values were plotted for 32 primary tumors (T) and paired, adjacent nontumor tissue samples (NT); samples from the same patient are linked with a straight line. ∗P < 0.0001, paired t-test. The Journal of Molecular Diagnostics 2013 15, 498-507DOI: (10.1016/j.jmoldx.2013.03.004) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Assessment of methylation status for the SDC2 gene in 95 match-paired CRC tissues by bisulfite pyrosequencing. MtI values were plotted for primary tumor tissue (T) and paired, adjacent nontumor tissues (NT); samples from the same patient are linked with a straight line. ∗P < 0.0001, paired t-test. The Journal of Molecular Diagnostics 2013 15, 498-507DOI: (10.1016/j.jmoldx.2013.03.004) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 Methylation test results of SDC2 marker for detecting CRC in serum DNA. A: Methylation status of SDC2 gene is plotted as PMR values. B: ROC curves for SDC2 gene for detecting CRC using serum DNA are depicted. AUC = 0.927 is significant at P = 0.0001. The Journal of Molecular Diagnostics 2013 15, 498-507DOI: (10.1016/j.jmoldx.2013.03.004) Copyright © 2013 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions