The novel colorectal cancer biomarkers CDO1, ZSCAN18 and ZNF331 are frequently methylated across gastrointestinal cancers

Abstract

We have previously shown that gastrointestinal cancers display similar epigenetic aberrations. In a recent study, we identified frequently methylated genes for cholangiocarcinoma (CDO1, DCLK1, SFRP1 and ZSCAN18), where one of these genes, DCLK1, was also confirmed to be highly methylated in colorectal cancer. The aim of the present study was to determine whether these four genes, in addition to one gene found to be methylated in colon cancer cell lines (ZNF331), are commonly methylated across gastrointestinal malignancies, as well as explore their role as potential biomarkers. Quantitative methylation specific PCR (qMSP) of colorectal cancer (n=164) and normal colorectal mucosa (n=106) samples showed that all genes were frequently methylated in colorectal cancer (71-92%) with little or no methylation in normal mucosa (0-3%). Methylation of minimum two of these five genes identified 95% of the tumors with a specificity of 98%, and an area under the receiver operating characteristics curve (AUC) of 0.98. For gastric (n=25) and pancreatic (n=20) cancer, the same panel detected 92% and 90% of the tumors, respectively. Seventy-four cancer cell lines were further analyzed by qMSP and real time RT-PCR. In addition to the previously reported DCLK1, a high negative correlation between promoter DNA methylation and gene expression was observed for CDO1, ZNF331 and ZSCAN18. In conclusion, the high methylation frequency of these genes in colorectal- as well as in gastric-, pancreatic- and bile duct cancer confirmed an epigenetic similarity between gastrointestinal cancer types, and simultaneously demonstrated their potential as biomarkers, particularly for colorectal cancer detection.

Keywords: CDO1; DCLK1; DNA methylation; SFRP1; ZNF331; ZSCAN18; biomarker; cancer.

Figure 1

Promoter DNA methylation of candidate genes (a–e) in colorectal cancers and controls across test and validation sets. The scoring threshold is marked by a dotted line, and outliers are excluded for better visualization (DCLK1, n = 6; SFRP1 and ZSCAN18, n = 1). Abbreviations; PMR, percent of methylated reference. The results for DCLK1 have been published previously.

Figure 2

Promoter methylation frequencies of the candidate genes in gastrointestinal cancers and controls. For the “combined” column, a sample is considered methylation positive if a minimum of two of the five genes are methylated. Red: methylated; green: unmethylated; white: missing value. The methylation status for DCLK1 in colorectal cancer and normal samples, as well as the cholangiocarcinoma results for CDO1, DCLK1, SFRP1 and ZSCAN18, have been published previously., The results are included here to evaluate the performance across gastrointestinal cancer types.

Figure 3

Receiver operating characteristic (ROC) curves for the markers individually (a) and combined (b) in colorectal cancer versus controls. The results for DCLK1 have been published previously.

Figure 4

Expression of CDO1, ZNF331 and ZSCAN18 in four colon cancer cell lines before and after treatment with epigenetic drugs.