Virus Expression Database
Submitted by David Robertson (University of Manchester, United Kingdom) on Jun 10 2011
Platform: microarray – [HG-U133_Plus_2] Affymetrix GeneChip Human Genome HG-U133 Plus 2 Array [Brainarray Version 12]
Pubmed: 22046242
Summary Hepatitis C virus (HCV) is a global problem. To better understand HCV infection researchers employ in vitro HCV cell-culture (HCVcc) systems that use Huh-7 derived hepatoma cells that are particularly permissive to HCV infection. A variety of hyper-permissive cells have been subcloned for this purpose. In addition, subclones of Huh-7 which have evolved resistance to HCV are available. However, the mechanisms of susceptibility or resistance to infection among these cells have not been fully determined. In order to elucidate mechanisms by which hepatoma cells are susceptible or resistant to HCV infection we performed genome-wide expression analyses of six Huh-7 derived cell cultures (Huh-7, Huh-7.5.1, Huh-7.5.1c2, R1.09, R1.10 and R2.1) R that have different levels of permissiveness to infection. A great number of genes, representing a wide spectrum of functions are differentially expressed between cells. To focus our investigation, we identify host proteins from HCV replicase complexes, perform gene expression analysis of three HCV infected cells (infected Huh-7, Huh-7.5.1 and Huh-7.5.1c2) and conduct a detailed analysis of differentially expressed host factors by integrating a variety of data sources. Our results demonstrate that changes relating to susceptibility to HCV infection in hepatoma cells are linked to the innate immune response, secreted signal peptides and host factors that have a role in virus entry and replication. This work identifies both known and novel host factors that may influence HCV infection. Our findings build upon current knowledge of the complex interplay between HCV and the host cell, which could aid development of new antiviral strategies.
Six Huh-7 derived hepatoma cell types that have different levels of susceptibility to HCV infection in cell culture are used: Huh-7, Huh-7.5.1, Huh-7.5.1c2, R1.09, R1.10 and R2.1. Of these the first three (label starting Huh are susceptible to HCV infection and the latter three (label starting R are resistant to HCV infection. All cell types are derived from Huh-7. Huh-7.5.1 is a subclone of Huh-7.5 that in turn is a subclone of Huh-7. Huh-7.5.1c2 is a subclone of Huh-7.5.1. R1.09 and R1.10 are subclones of R1 that is inturn a sublone of Huh-7.5,1. R2.1 is a subclone of Huh-7.5.1.
| ID | Title | Cell Type | Timepoint | Reported Virus | Virus Species | Exclusion Reason |
|---|---|---|---|---|---|---|
| GSM740159 | Huh-7.5.1c2 uninfected 96hr study1 sample1 | hepatoma cell line  [Huh-7.5.1  ] |
96 hrs | uninfected | Uninfected | |
| GSM740160 | Huh-7.5.1c2 uninfected 96hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
96 hrs | uninfected | Uninfected | |
| GSM740161 | Huh-7.5.1c2 uninfected 96hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
96 hrs | uninfected | Uninfected | |
| GSM740162 | Huh-7.5.1 uninfected 120hr study1 sample1 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | uninfected | Uninfected | |
| GSM740163 | Huh-7.5.1 uninfected 120hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | uninfected | Uninfected | |
| GSM740164 | Huh-7.5.1 uninfected 120hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | uninfected | Uninfected | |
| GSM740165 | Huh-7 uninfected 168hr study1 sample1 | hepatoma cell line [Huh-7 ] |
168 hrs | uninfected | Uninfected | |
| GSM740166 | Huh-7 uninfected 168hr study1 sample2 | hepatoma cell line [Huh-7 ] |
168 hrs | uninfected | Uninfected | |
| GSM740167 | Huh-7 uninfected 168hr study1 sample3 | hepatoma cell line [Huh-7 ] |
168 hrs | uninfected | Uninfected | |
| GSM740168 | Huh-7.5.1c2 infected 96hr study1 sample1 | hepatoma cell line [Huh-7.5.1 ] |
96 hrs | HCV | Hepacivirus C | |
| GSM740169 | Huh-7.5.1c2 infected 96hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
96 hrs | HCV | Hepacivirus C | |
| GSM740170 | Huh-7.5.1c2 infected 96hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
96 hrs | HCV | Hepacivirus C | |
| GSM740171 | Huh-7.5.1 infected 120hr study1 sample1 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | HCV | Hepacivirus C | |
| GSM740172 | Huh-7.5.1 infected 120hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | HCV | Hepacivirus C | |
| GSM740173 | Huh-7.5.1 infected 120hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
120 hrs | HCV | Hepacivirus C | |
| GSM740174 | Huh-7 infected 168hr study1 sample1 | hepatoma cell line [Huh-7 ] |
168 hrs | HCV | Hepacivirus C | |
| GSM740175 | Huh-7 infected 168hr study1 sample2 | hepatoma cell line [Huh-7 ] |
168 hrs | HCV | Hepacivirus C | |
| GSM740176 | Huh-7 infected 168hr study1 sample3 | hepatoma cell line [Huh-7 ] |
168 hrs | HCV | Hepacivirus C | |
| GSM740177 | Huh-7.5.1c2 uninfected 20hr study1 sample1 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740178 | Huh-7.5.1c2 uninfected 20hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740179 | Huh-7.5.1c2 uninfected 20hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740180 | Huh-7.5.1 uninfected 20hr study1 sample1 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740181 | Huh-7.5.1 uninfected 20hr study1 sample2 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740182 | Huh-7.5.1 uninfected 20hr study1 sample3 | hepatoma cell line [Huh-7.5.1 ] |
20 hrs | uninfected | Uninfected | |
| GSM740183 | Huh-7 uninfected 20hr study1 sample1 | hepatoma cell line [Huh-7 ] |
20 hrs | uninfected | Uninfected | |
| GSM740184 | Huh-7 uninfected 20hr study1 sample2 | hepatoma cell line [Huh-7 ] |
20 hrs | uninfected | Uninfected | |
| GSM740185 | Huh-7 uninfected 20hr study1 sample3 | hepatoma cell line [Huh-7 ] |
20 hrs | uninfected | Uninfected | |
| GSM740186 | R1.09 uninfected study2 sample1 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740187 | R1.09 uninfected study2 sample2 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740188 | R1.09 uninfected study2 sample3 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740189 | R1.10 uninfected study2 sample1 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740190 | R1.10 uninfected study2 sample2 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740191 | R1.10 uninfected study2 sample3 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740192 | R2.1 uninfected study2 sample1 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740193 | R2.1 uninfected study2 sample2 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740194 | R2.1 uninfected study2 sample3 | hepatoma cell line |
uninfected | Uninfected | ||
| GSM740195 | Huh-7.5.1 uninfected study2 sample1 | hepatoma cell line [Huh-7.5.1 ] |
uninfected | Uninfected | ||
| GSM740196 | Huh-7.5.1 uninfected study2 sample2 | hepatoma cell line [Huh-7.5.1 ] |
uninfected | Uninfected | ||
| GSM740197 | Huh-7.5.1 uninfected study2 sample3 | hepatoma cell line [Huh-7.5.1 ] |
uninfected | Uninfected |