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| Status |
Public on Oct 22, 2012 |
| Title |
The blood transcriptional signature of chronic HCV [Affymetrix data] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
This study characterizes the effects of chronic Hepatitis C virus (HCV) infection on gene expression by analyzing blood samples from 10 treatment-naive HCV patients and 6 healthy volunteers.
Differential expression analysis of microarray data from peripheral blood mononuclear cells (PBMCs) identified a 136 gene signature, including 66 genes elevated in infected individuals. Most of the up-regulated genes were associated with interferon (IFN) activity (including members of the OAS and MX families, ISG15 and IRF7), suggesting an ongoing immune response. This HCV signature was also found to be consistently enriched in many other viral infection and vaccination datasets. Validation of these genes was carried out using a second cohort composed of 5 HCV patients and 5 healthy volunteers, confirming the up-regulation of the IFN signature. In summary, this is the first study to directly compare blood transcriptional profiles from HCV patients with healthy controls. The results show that chronic HCV infection has a pronounced effect on gene expression in PBMCs of infected individuals, and significantly elevates the expression of a subset of interferon-stimulated genes.
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| Overall design |
Whole blood was collected from a group of 10 patients who were infected with genotype 1 hepatitis C, before initiation of treatment at the Indiana University School of Medicine. Control blood samples were harvested from healthy student volunteers. Peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of the cohort using centrifugation through a 10-ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ), and RNA was isolated within a few hours. RNA was then processed according to the protocols recommended by Affymetrix (Santa Clara, CA), and run on an Affymextrix Human Genome U133 array.
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| Contributor(s) |
Bolen CR, Robek MD, Brodsky L, Schulz V, Lim J, Taylor MW, Kleinstein SH |
| Citation(s) |
23067362 |
| |
| Submission date |
Aug 17, 2012 |
| Last update date |
Aug 10, 2018 |
| Contact name |
Christopher Bolen |
| E-mail(s) |
[email protected]
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| Organization name |
Yale University
|
| Department |
Pathology
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| Lab |
Steven Kleinstein
|
| Street address |
300 George Street, Suite 505
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platforms (1) |
| GPL96 |
[HG-U133A] Affymetrix Human Genome U133A Array |
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| Samples (18)
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| This SubSeries is part of SuperSeries: |
| GSE40224 |
The blood transcriptional signature of chronic HCV |
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| Relations |
| BioProject |
PRJNA173226 |
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