Transcriptomics

Dataset Information

45

Transcription profiling by array of human hepatitis B virus (HBV) and hepatitis C virus (HCV) induced hepatocellular (HCC) carcinoma and surrounding noncancerous liver tissue.


ABSTRACT: Chronic infections by hepatitis B virus (HBV) and hepatitis C virus (HCV) appear to be the most significant causes of hepatocellular carcinoma (HCC). Aberrant promoter methylation is known to be deeply involved in cancer, including HCC. In this study, we analyzed aberrant promoter methylation on genome-wide scale in 6 HCCs including 3 HBV-related and 3 HCV-related HCCs, 6 matched noncancerous liver tissues and 3 normal liver tissues by methylated DNA immunoprecipitation-on-chip analysis. Candidate genes with promoter methylation were detected more frequently in HCV-related HCC. Candidate genes methylated preferentially to HBV-related or HCV-related HCCs were detected and selected, and methylation levels of the selected genes were validated using 125 liver tissue samples, including 61 HCCs (28 HBV-related HCCs and 33 HCV-related HCCs) and matched 59 matched noncancerous livers, and 5 normal livers, by quantitative methylation analysis using MALDI-TOF mass spectrometry. Among analyzed genes, preferential methylation in HBV-related HCC was validated in 1 gene only. However, 15 genes were found methylated preferentially in HCV-related HCC, which was independent from age. Hierarchical clustering of HCC using these 15 genes stratified HCV-related HCC as a cluster of frequently methylated samples. The 15 genes included genes inhibitory to cancer-related signaling such as RAS/RAF/ERK and Wnt/b-catenin pathways. It was indicated that genes methylated preferentially in HCV-related HCC exist, and it was suggested that DNA methylation might play an important role in HCV-related HCC by silencing cancer-related pathway inhibitors. we analyzed aberrant promoter methylation in 6 HCC clinical samples (including 3 HBV-related HCCs and 3 HCV-related HCCs) and their matched noncancerous tissues on genome-wide scale by the method. Candidate regions of promoter methylation preferentially to HBV-related HCC and HCV-related HCC were selected, and the methylation levels of these genes were measured quantitatively using MALDI-TOF mass spectrometry. Expression levels of these 6 pairs of HCC and 4 more pairs of HCCs and surrounding noncancerous tissues were analyzed by expression array and are reported in this Series.

This experiment was reloaded in November 2010 after additional curation

REANALYSED by: E-GEOD-19665

ORGANISM(S): Homo sapiens  

SUBMITTER: Genta Nagae   Ying-Bing Deng  Hiroyuki Aburatani  Atsushi Kaneda 

PROVIDER: E-GEOD-19665 | ArrayExpress | 2010-07-06

SECONDARY ACCESSION(S): GSE19665PRJNA122481

REPOSITORIES: GEO, ArrayExpress

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Publications

Identification of genes preferentially methylated in hepatitis C virus-related hepatocellular carcinoma.

Deng Ying-Bing YB   Nagae Genta G   Midorikawa Yutaka Y   Yagi Koichi K   Tsutsumi Shuichi S   Yamamoto Shogo S   Hasegawa Kiyoshi K   Kokudo Norihiro N   Aburatani Hiroyuki H   Kaneda Atsushi A  

Cancer science 20100227 6


Chronic infections by hepatitis B virus (HBV) and hepatitis C virus (HCV) appear to be the most significant causes of hepatocellular carcinoma (HCC). Aberrant promoter methylation is known to be deeply involved in cancer, including in HCC. In this study, we analyzed aberrant promoter methylation by methylated DNA immunoprecipitation-on-chip analysis on a genome-wide scale in six HCCs including three HBV-related and three HCV-related HCCs, six matched noncancerous liver tissues, and three normal  ...[more]

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