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| Status |
Public on Oct 22, 2012 |
| Title |
The blood transcriptional signature of chronic HCV [Illumina 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 |
Treatment-naïve HCV patients were recruited by hepatologists in the outpatient hepatitis clinic within the Yale Liver Center. Healthy volunteers were recruited from Yale’s PhenoGenetic Cohort of Healthy controls. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) centrifugation. Total RNA was isolated from PBMCs using an RNeasy kit (Qiagen, Valencia, CA), and the quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on an Agilent Bioanalyzer. All subsequent processing, hybridization to the Illumina HumanHT-12 microarray, and quality control analyses were carried out by the Yale Center for Genome Analysis using standard protocols.
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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 20, 2012 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Christopher Bolen |
| E-mail(s) |
cbolen1@gmail.com
|
| Organization name |
Yale University
|
| Department |
Pathology
|
| Lab |
Steven Kleinstein
|
| Street address |
300 George Street, Suite 505
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE40224 |
The blood transcriptional signature of chronic HCV |
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| Relations |
| BioProject |
PRJNA173227 |
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