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| Status |
Public on Jan 01, 2011 |
| Title |
Transcriptional profiling of CD4 T-cells in HIV-1 infected patients |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
HIV-1 elite controllers maintain undetectable levels of viral replication in the absence of antiretroviral therapy, but their underlying immunological and virological characteristics may vary. Here, we used a whole-genome transcriptional profiling approach to characterize gene expression signatures of CD4 T cells from an unselected cohort of elite controllers. In the majority of elite controllers, transcriptional profiles were similar to HAART-treated patients, while being different from HIV-1 negative persons. Yet, a smaller proportion of elite controllers showed an opposite gene expression pattern that was indistinguishable from HIV-1 negative persons, but different from HAART-treated individuals. Elite controllers with this gene expression signature had significantly higher CD4 T cell counts, smaller levels of HIV-1-specific CD8+ T cell responses and tended to have lower residual HIV-1 viremia as determined by ultra-sensitive single-digit PCR, but did not differ from other elite controllers in terms of HLA class I alleles, age or sex. Thus, these data identify a specific subgroup of elite controllers whose clinical, immunological and gene expression characteristics approximate those of HIV-1 negative persons.
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| Overall design |
PBMC from study persons were stained with monoclonal antibodies against CD3, CD4 and HLA-DR, and subsequently subjected to live sorting at 70 psi using an ARIA cell sorting device (Becton Dickinson) located in a specifically designated biosafety cabinet. Following mRNA extraction form the sorted cells (RNAeasy kit, Qiagen), whole genome transcriptional profiling was performed using WG-DASL microarrays (Illumina) according to standard protocols. We included an unselected cohort of elite controllers (n = 12) and two background populations of HIV-1 negative persons (n = 9) and HIV-1 infected persons effectively treated with HAART (n = 14). Four replicates were included in the study.
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| Contributor(s) |
Vigneault F, Woods M, Buzon M, Pereyra F, Toth I, Church G, Rosenberg ES, Martinez-Picado J, Telenti A, Yu XG, Lichterfeld M |
| Citation(s) |
21177805 |
| Submission date |
Aug 30, 2010 |
| Last update date |
May 14, 2015 |
| Contact name |
Matthew Woods |
| E-mail(s) |
mwoods3@partners.org
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| Organization name |
The Ragon Institute of MGH, MIT, and Harvard
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| Department |
Computational Biology Core
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| Street address |
149 13th Street
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| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
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| Platforms (1) |
| GPL8432 |
Illumina HumanRef-8 WG-DASL v3.0 |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA130609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23879_RAW.tar |
9.7 Mb |
(http)(custom) |
TAR |
| GSE23879_non-normalized.txt.gz |
5.6 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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