Comparison of HCV-associated gene expression and cell signaling pathways in cells with or without HCV replicon and in replicon-cured cells.
BACKGROUND
Hepatitis C virus (HCV) replication is affected by several host factors. Here, we screened host genes and molecular pathways that are involved in HCV replication by comprehensive analyses using two genotypes of HCV replicon-expressing cells, their cured cells and naïve Huh7 cells.


METHODS
Huh7 cell lines that stably expressed HCV genotype 1b or 2a replicon were used. The cured cells were established by treating HCV replicon cells with interferon-alpha. Expression of 54,675 cellular genes was analyzed by GeneChip DNA microarray. The data were analyzed by using the KEGG Pathway database.


RESULTS
Hierarchical clustering analysis showed that the gene-expression profiles of each cell group constituted clear clusters of naïve, HCV replicon-expressed, and cured cell lines. The pathway process analysis between the replicon-expressing and the cured cell lines identified significantly altered pathways, including MAPK, steroid biosynthesis and TGF-beta signaling pathways, suggesting that these pathways were affected directly by HCV replication. Comparison of cured and naïve Huh7 cells identified pathways, including steroid biosynthesis and sphingolipid metabolism, suggesting that these pathways were required for efficient HCV replication. Cytoplasmic lipid droplets were obviously increased in replicon-expressing and cured cells as compared to naïve cells. HCV replication was significantly suppressed by peroxisome proliferator-activated receptor (PPAR)-alpha agonists but augmented by PPAR-gamma agonists.


CONCLUSIONS
Comprehensive gene expression and pathway analyses show that lipid biosynthesis pathways are crucial to support proficient virus replication. These metabolic pathways could constitute novel antiviral targets against HCV.
Nishimura-Sakurai
Yuki
Y
Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan.
Sakamoto
Naoya
N
Mogushi
Kaoru
K
Nagaie
Satoshi
S
Nakagawa
Mina
M
Itsui
Yasuhiro
Y
Tasaka-Fujita
Megumi
M
Onuki-Karakama
Yuko
Y
Suda
Goki
G
Mishima
Kako
K
Yamamoto
Machi
M
Ueyama
Mayumi
M
Funaoka
Yusuke
Y
Watanabe
Takako
T
Azuma
Seishin
S
Sekine-Osajima
Yuko
Y
Kakinuma
Sei
S
Tsuchiya
Kiichiro
K
Enomoto
Nobuyuki
N
Tanaka
Hiroshi
H
Watanabe
Mamoru
M
D018929:Cell Culture Techniques; D002460:Cell Line; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D005814:Genes, Viral / Q000235:genetics*; D016174:Hepacivirus / Q000502:physiology*; D006801:Humans; D050356:Lipid Metabolism / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis; D012093:Replicon / Q000235:genetics*; D015398:Signal Transduction / Q000502:physiology*; D014779:Virus Replication / Q000502:physiology*