Construction and Validation of Novel Diagnostic and Prognostic DNA Methylation Signatures for Hepatocellular Carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the most prevalent life-threatening human cancers and the leading cause of cancer-related mortality, with increased global incidence within the last decade. Identification of effective diagnostic and prognostic biomarkers would enable reliable risk stratification and efficient screening of highrisk patients, thereby facilitating clinical decision-making. Herein, we performed a comprehensive, robust DNA methylation analysis based on genome-wide DNA methylation profiling. We constructed a diagnostic signature with five DNA methylation markers, which precisely distinguished HCC patients from normal controls. Cox regression and LASSO analysis were applied to construct a prognostic signature with four DNA methylation markers. A one-to-one correlation analysis was carried out between genes of the whole genome and our prognostic signature. Exploration of the biological function and the role of the underlying significantly correlated genes was conducted. A mixed dataset of 463 HCC patients and 253 normal controls, derived from six independent datasets, was used to valid the diagnostic signature. Results showed a specificity of 96.84% and sensitivity of 96.77%. Class scores for the diagnostic signature were significantly different between normal controls, individuals with liver diseases, and HCC patients. The present signature has the potential to serve as a biomarker to monitor health in normal controls. Additionally, HCC patients were successfully separated into low-risk and high-risk groups by the prognostic signature, with a better prognosis for patients in the low-risk group. Kaplan-Meier and ROC analysis confirmed that the prognostic signature performed well. We found eight of the top ten genes to positively correlate with risk scores of the prognostic signature, and to be involved in cell cycle regulation. This eight-gene panel also served as a prognostic signature. The robust evidence presented in this study therefore demonstrates the effectiveness of the prognostic signature. In summary, we constructed diagnostic and prognostic signatures,

epiLiver a novel tumor specific, high throughput and cost-effective blood test for specific detection of liver cancer (HCC)

“…We compared “HCC-spec” and “HCC-detect” DNA methylation markers (Fig. 3A) to two other extremely promising sets of HCC biomarkers that were recently described [22] [19] (Fig. 3B,C) using DNA methylation values for the respective CGs in Illumina 450K arrays from the 11701 samples described above.…”

“…Heat map presentation of the methylation values for shortlisted HCC detection CG sites described here ( A ) in Liu et al[22] ( B) and Zhang et al, (C) [19]. …”

“…Comparisons of cancer type specificity of "HCC-detect and spec" combination and two previously published biomarkers. Heat map presentation of the methylation values for shortlisted HCC detection CG sites described here (A) in Liu et al[22] (B) and Zhang et al, (C)[19].…”

epiLiver a novel tumor specific, high throughput and cost-effective blood test for specific detection of liver cancer (HCC)

“…We compared "HCC-spec" and "HCC-detect" DNA methylation markers (Fig. 3A) to two other extremely promising sets of HCC biomarkers that were recently described [22] [19] (Fig. 3B,C) using DNA methylation values for the respective CGs in Illumina 450K arrays from the 11701 samples described above.…”

“…E. scattered plot of "HCC-detect" Methylation score (each spot represents one sample) in healthy blood (n=968), healthy liver tissue (n=16), liver disease (n=158), nonliver healthy tissues (n=234), NAT to nonHCC tumors Figure 3 Comparisons of cancer type speci city of "HCC-detect and spec" combination and two previously published biomarkers. Heat map presentation of the methylation values for shortlisted HCC detection CG sites described here (A) in Liu et al [22] (B) and Zhang et al, (C) [19].…”