System-based proteomic analysis of the interferon response in human liver cells.
BACKGROUND
Interferons (IFNs) play a critical role in the host antiviral defense and are an essential component of current therapies against hepatitis C virus (HCV), a major cause of liver disease worldwide. To examine liver-specific responses to IFN and begin to elucidate the mechanisms of IFN inhibition of virus replication, we performed a global quantitative proteomic analysis in a human hepatoma cell line (Huh7) in the presence and absence of IFN treatment using the isotope-coded affinity tag (ICAT) method and tandem mass spectrometry (MS/MS).


RESULTS
In three subcellular fractions from the Huh7 cells treated with IFN (400 IU/ml, 16 h) or mock-treated, we identified more than 1,364 proteins at a threshold that corresponds to less than 5% false-positive error rate. Among these, 54 were induced by IFN and 24 were repressed by more than two-fold, respectively. These IFN-regulated proteins represented multiple cellular functions including antiviral defense, immune response, cell metabolism, signal transduction, cell growth and cellular organization. To analyze this proteomics dataset, we utilized several systems-biology data-mining tools, including Gene Ontology via the GoMiner program and the Cytoscape bioinformatics platform.


CONCLUSIONS
Integration of the quantitative proteomics with global protein interaction data using the Cytoscape platform led to the identification of several novel and liver-specific key regulatory components of the IFN response, which may be important in regulating the interplay between HCV, interferon and the host response to virus infection.
Yan
Wei
W
Institute for Systems Biology, Seattle, WA 98103, USA. wyan@systemsbiology.org
Lee
Hookeun
H
Yi
Eugene C
EC
Reiss
David
D
Shannon
Paul
P
Kwieciszewski
Bartlomiej K
BK
Coito
Carlos
C
Li
Xiao-jun
XJ
Keller
Andrew
A
Eng
Jimmy
J
Galitski
Timothy
T
Goodlett
David R
DR
Aebersold
Ruedi
R
Katze
Michael G
MG
D045744:Cell Line, Tumor; D019295:Computational Biology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects*; D022781:Hepatocytes / Q000187:drug effects* / Q000276:immunology / Q000378:metabolism* / Q000821:virology; D006801:Humans; D007372:Interferons / Q000494:pharmacology*; D013058:Mass Spectrometry; D011485:Protein Binding; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D040901:Proteomics; D015398:Signal Transduction / Q000187:drug effects; D012984:Software; D013379:Substrate Specificity; D049490:Systems Biology; D014780:Viruses / Q000276:immunology
D020543:Proteome; D007372:Interferons