Abstract 2959: Differential DNA methylation in peripheral blood DNA as a biomarker of hepatocellular carcinoma risk

• Published in: Cancer research (Chicago, Ill.) Ill.), 2015-08, Vol.75 (15_Supplement), p.2959-2959
• Main Authors: Lubecka-Pietruszewska, Katarzyna, Kurzava, Lucinda, Buvala, Hannah, Flower, Kirsty, Gawrieh, Samer, Mansfield, Jennifer, Chalasani, Naga, Flanagan, James M., Stefanska, Barbara
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2015-2959

Hepatocellular carcinoma (HCC), one of the most prevalent types of primary liver cancer, is the sixth most common cancer worldwide and the third leading cause of cancer death with rising mortality and morbidity rates. As late onset of HCC accounts for late diagnosis and poor prognosis and early detection increases cure rate from 5% to 80%, identifying reliable and quantifiable biomarkers of risk prediction is of high interest. Aberrations in the DNA methylation patterns, an important early event in carcinogenesis, have been shown to differentiate HCC tumors from normal tissues. However, these changes as predictive markers would have a high application in clinics only if detectable by minimally invasive tests like blood test. In the present study, we performed a comprehensive evaluation of DNA methylation profiles in blood DNA collected before diagnosis with HCC. Aberrant methylation was investigated in DNA isolated from blood of 21 HCC patients (cases) who provided samples between 1-4 years prior to diagnosis and 21 controls enrolled by the Indiana Biobank of Indiana CTSI. Cases were matched with controls for gender, age, ethnicity, hepatitis C infection, and diabetes. We used Infinium Human Methylation 450K BeadChip array for genome-wide DNA methylation analysis and pyrosequencing for validation of DNA methylation differences. We found 966 probes differentially methylated between cases and controls with p0.5. Among these significant changes, 732 CpG sites are hypomethylated in HCC cases compared to matched controls and include 130 CpGs corresponding to 75 genes with delta beta value (differential methylation) ≥0.1. Forty six CpG sites out of 234 significantly hypermethylated probes show delta beta value ≥0.1 and correspond to 46 genes. Functional analyses using GO, KEGG and DAVID knowledgebase indicates that hypomethylated genes are associated with Wnt signaling, cell adhesion, blood coagulation, and regulation of transcription, whereas hypermethylated genes are enriched with cytoskeleton organization and small GTPase mediated signal transduction. One of the genes hypomethylated in blood DNA of HCC cases prior to diagnosis is TET1 that was found to be 8-fold overexpressed in HCC tumors in our previous studies and implicated in gene-specific hypomethylation. Interestingly, 75% of differentially methylated sites in blood DNA of HCC cases are hypomethylated prior to diagnosis. Validation by pyrosequencing of four