SCTR hypermethylation is a diagnostic biomarker in colorectal cancer

Abstract

Diagnostic markers for both colorectal cancer (CRC) and its precursor lesions are lacking. Although aberrant methylation of the secretin receptor (SCTR) gene was observed in CRC, the diagnostic performance has not been evaluated. Therefore, this study aimed to assess and verify the diagnostic value of SCTR methylation of CRC and its precursor lesions through integrating the largest methylation data. The diagnostic performance of SCTR methylation was analyzed in the discovery set from The Cancer Genome Atlas (TCGA) CRC methylation data (N = 440), and verified in a large-scale test set (N = 938) from the Gene Expression Omnibus (GEO). Targeted bisulfite sequencing analysis was developed and applied to detect the methylation status of SCTR in our independent validation set (N = 374). Our findings revealed that the SCTR gene was frequently hypermethylated at its CpG islands in CRC. In the TCGA discovery set, the diagnostic score was constructed using 4 CpG sites (cg01013590, cg20505223, cg07176264, and cg26009192) and achieved high diagnostic performance (area under the ROC curve [AUC] = 0.964). In the GEO test set, the diagnostic score had robust diagnostic ability to distinguish CRC (AUC = 0.948) and its precursor lesions (AUC = 0.954) from normal samples. Moreover, hypermethylation of the SCTR gene was also found in cell-free DNA samples collected from CRC patients, but not in those from healthy controls. In the validation set, consistent results were observed using the targeted bisulfite sequencing array. Our study highlights that hypermethylation at CpG islands of the SCTR gene is a potential diagnostic biomarker in CRCs and its precursor lesions.

Keywords: SCTR; DNA methylation; biomarker; colorectal cancer; diagnosis.

FIGURE 1

Overall workflow of the various analyses in different methylation datasets

FIGURE 2

Differential methylation analysis for 10 CpG sites of the SCTR gene between colorectal cancer tissues and normal tissues in TCGA discovery set. Gene promoter was defined as the region containing TSS200, TSS1500, 5′UTR, and the first exon. Symbols indicated statistical significance for the t test: ns, P > .05; **** P ≤ .0001

FIGURE 3

Diagnostic performance of the 4‐CpG diagnostic score for colorectal cancer and its precursors. ROC curves of the diagnostic score constructed by the logistic regression model in (A) the TCGA discovery set, (B) the GEO test set A, and (C) the GEO test set B. The blue point indicates sensitivity and specificity at the fixed cut‐off value of 6.154

FIGURE 4

Methylation status of cg20505223 in the validation set. A, Differential methylation analysis of cg20505223 between 272 colorectal cancer tissues and 23 normal tissues, **** P ≤ .0001. B, Receiver operating characteristic curve analysis and Youden index analysis of cg20505223 for discriminating colorectal cancer tissues and normal tissues. The blue point indicates sensitivity and specificity at the cut‐off value of 0.071

FIGURE 5

Methylation levels of cg20505223 in white blood cell samples from 29 colorectal cancer patients and 29 healthy controls. * P ≤ .05

FIGURE 6

Average methylation levels of the SCTR gene at different disease stages during neoplastic progression. * P ≤ .05