Molecular signature in three types of hepatocellular carcinoma with different viral origin by oligonucleotide microarray.
Chronic infection with hepatitis B or C virus (HBV or HCV) is the most clearly established risk factor for hepato-cellular carcinoma (HCC). One type of HCC (non-B, non-C HCC) also appears to develop in patients negative for both HBV and HCV. Using a supervised learning method, we investigated gene expression in 11 non-B, non-C HCCs with high-density oligonucleotide microarrays, and compared the patterns of gene expression with those of HBV-infected HCCs (B-type HCCs) and HCV-infected HCCs (C-type HCCs) in the previous dataset. Our gene selection identified 112 and 64 genes that were differentially expressed in non-B, non-C HCC in comparison with B- and C-type HCCs, respectively. In both gene selections, we found that the false discovery rate, the percentage of genes identified by chance, was less than 5%. Additionally, in combination with the previous data, our present data revealed a set of genes specific to each type of B- and C-type HCCs and non-B, non-C HCC. Among these, an interferon-induced gene, IFI27, was differentially expressed among all three types of HCCs, and this result was confirmed by RT-PCR. Thus, our present study provides a framework to characterize the molecular features in the three subtypes of HCC with different viral origin.
Iizuka
Norio
N
Department of Bioregulatory Function, Yamaguchi University School of Medicine, Ube, Yamaguchi 755-8505, Japan.
Oka
Masaaki
M
Yamada-Okabe
Hisafumi
H
Hamada
Kenji
K
Nakayama
Hironobu
H
Mori
Naohide
N
Tamesa
Takao
T
Okada
Toshimasa
T
Takemoto
Norikazu
N
Matoba
Katsuhiro
K
Takashima
Motonari
M
Sakamoto
Katsuhiko
K
Tangoku
Akira
A
Miyamoto
Takanobu
T
Uchimura
Shunji
S
Hamamoto
Yoshihiko
Y
D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000821:virology*; D003062:Codon; D018076:DNA, Complementary / Q000378:metabolism; D015536:Down-Regulation; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D016174:Hepacivirus / Q000235:genetics; D006515:Hepatitis B virus / Q000235:genetics; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000821:virology*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015854:Up-Regulation
D003062:Codon; D018076:DNA, Complementary; D009841:Oligonucleotides; D012313:RNA