Discovery and validation of DNA hypomethylation biomarkers for liver cancer using HRM-specific probes.
Poor prognosis of hepatocellular carcinoma (HCC) associated with late diagnosis necessitates the development of early diagnostic biomarkers. We have previously delineated the landscape of DNA methylation in HCC patients unraveling the importance of promoter hypomethylation in activation of cancer- and metastasis-driving genes. The purpose of the present study was to test the feasibility that genes that are hypomethylated in HCC could serve as candidate diagnostic markers. We use high resolution melting analysis (HRM) as a simple translatable PCR-based method to define methylation states in clinical samples. We tested seven regions selected from the shortlist of genes hypomethylated in HCC and showed that HRM analysis of several of them distinguishes methylation states in liver cancer specimens from normal adjacent liver and chronic hepatitis in the Shanghai area. Such regions were identified within promoters of neuronal membrane glycoprotein M6-B (GPM6B) and melanoma antigen family A12 (MAGEA12) genes. Differences in HRM in the immunoglobulin superfamily Fc receptor (FCRL1) separated invasive tumors from less invasive HCC. The identified biomarkers differentiated HCC from chronic hepatitis in another set of samples from Dhaka. Although the main thrust in DNA methylation diagnostics in cancer is on hypermethylated genes, our study for the first time illustrates the potential use of hypomethylated genes as markers for solid tumors. After further validation in a larger cohort, the identified DNA hypomethylated regions can become important candidate biomarkers for liver cancer diagnosis and prognosis, especially in populations with high risk for HCC development.
Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada.
Barbara
B
Stefanska
Aurelie
A
Bouzelmat
Jian
J
Huang
Matthew
M
Suderman
Michael
M
Hallett
Ze-Guang
ZG
Han
Mamun
M
Al-Mahtab
Sheikh Mohammad Fazle
SM
Akbar
Wasif Ali
WA
Khan
Rubhana
R
Raqib
Moshe
M
Szyf
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000951:Antigens, Neoplasm / Q000235:genetics; D014408:Biomarkers, Tumor / Q000235:genetics*; D006528:Carcinoma, Hepatocellular / Q000175:diagnosis / Q000235:genetics*; D019175:DNA Methylation; D015342:DNA Probes / Q000235:genetics*; D005260:Female; D019694:Hepatitis B, Chronic / Q000175:diagnosis / Q000235:genetics; D006801:Humans; D008113:Liver Neoplasms / Q000175:diagnosis / Q000235:genetics*; D008297:Male; D008562:Membrane Glycoproteins / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D012680:Sensitivity and Specificity; D044366:Transition Temperature; D055815:Young Adult
D000951:Antigens, Neoplasm; D014408:Biomarkers, Tumor; D015342:DNA Probes; C551993:FCRL1 protein, human; C484160:GPM6B protein, human; C409589:MAGEA12 protein, human; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins