Carcinogenetic risk estimation based on quantification of DNA methylation levels in liver tissue at the precancerous stage

Abstract

For appropriate surveillance of patients at the precancerous stage for hepatocellular carcinomas (HCCs), carcinogenetic risk estimation is advantageous. The aim of our study was to establish criteria for such estimation based on DNA methylation profiling. The DNA methylation status of 203 CpG sites on 25 bacterial artificial chromosome (BAC) clones, whose DNA methylation status had been proven to discriminate samples of noncancerous liver tissue obtained from patients with HCC (N) from normal liver tissue (C) samples by BAC array-based methylated CpG island amplification, was evaluated quantitatively using pyrosequencing. The 45 CpG sites whose DNA methylation levels differed significantly between C and N in the learning cohort (n=22) were identified. The criteria combining DNA methylation status for the 30 regions including the 45 CpG sites were able to diagnose N as being at high risk of carcinogenesis with 100% sensitivity and specificity in the learning cohort and 95.6% sensitivity and 100% specificity in the validation (n=90) cohort. DNA methylation status for the 30 regions in N samples was significantly correlated with the outcome of patients with HCCs, indicating that clinicopathologically valid DNA methylation alterations have already accumulated at the precancerous stage. The DNA methylation status of the 30 regions did not depend on the presence or absence of hepatitis virus infection, or the status of noncancerous liver tissue (chronic hepatitis or cirrhosis). These criteria may be applicable for carcinogenetic risk estimation using liver biopsy specimens obtained from patients who are followed up because of chronic liver diseases.

Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: Its correlation with smoking history and chronic obstructive pulmonary disease

“…In fact, many patients in Cluster I actually suffered from obstructive ventilation impairment, and histological findings compatible with emphysema and lung fibrosis were observed in their N samples. Moreover, recurrent inflammation is generally associated with COPD,30 and histological findings compatible with respiratory bronchiolitis20,21 were actually observed in the lungs of patients belonging to Cluster I. Inflammation is known to be one of the major causes of DNA methylation alterations in precancerous conditions in various organs, such as chronic hepatitis16,17 and chronic pancreatitis 31,32…”

Multilayer‐omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome

“…The PCR and sequencing primers were designed using Pyrosequencing Assay Design Software ver.1.0 (QIAGEN, Hilden, Germany). To overcome any PCR bias, we optimized the annealing temperature as described previously 24. Each of the primer sequences and PCR conditions are given in Supporting Information Figure S2.…”

DNA Methylation of MicroRNA-124a Is a Potential Risk Marker of Colitis-Associated Cancer in Patients with Ulcerative Colitis

“…Moreover, significantly higher methylation levels of miR-124a-3 were present in the rectal mucosa of UC patients with pancolitis and long-standing duration that were major epidemiological risk factors for CAC development. To our knowledge, this is the first study to demonstrate that quantitative methylation levels of microRNA genes correlate with risk factors for CAC development and The degree of aberrant DNA methylation accumulated in non-cancerous tissues has been correlated with risk for gastric and liver cancer [24][25][26]. From the standpoint of inflammation-associated cancers, we quantified methylation levels of miR-124a-3 in the rectal mucosa of UC patients, and patients with high methylation levels were found to have two major epidemiological risk factors and methylation of ER.…”