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| Status |
Public on Jan 01, 2013 |
| Title |
HIV downregulates interferon stimulated genes in primary macrophages. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
HIV is able to outpace the innate immune response, including the response mediated by interferon (IFN), to establish a productive infection. However, monocyte derived macrophages (MDMs) may be protected from HIV infection by treatment with type I IFN before virus exposure. The ability of HIV to modulate the type I IFN-mediated innate immune response when it encounters a cell that has already been exposed to IFN was investigated.
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| Overall design |
To investigate the presence of HIV on an established IFN response, MDMs were subjected to four different conditions: (1) IFN-treated only, (2) IFN-treated followed by HIV infection, (3) HIV infected only, and (4) a mock-treated and mock-infected control. Microarray gene expression analysis was performed on a total of 24 samples derived from the 4 conditions assessed at 3 time points (1, 4 and 8 days following treatment/infection) for both IFN-α2 or -ω. Initially, ISGs were identified as those that were upregulated greater than 2-fold by IFN alone (condition 1) at both Days 4 and 8. Then, the IFN-treated condition was compared to the IFN-treated followed by HIV-infection condition in order to identify those ISGs that were downregulated at least 1.5-fold by the presence of HIV at both days. Assuming that it would be counterproductive for HIV infection by itself to induce the expression of ISGs with putative anti-HIV effects, those ISGs that were upregulated greater than 2-fold in the HIV control were removed. Finally, ISGs that passed these filters and were concordant with both IFN-treatments (IFN-α2 and -ω) were identified and corresponded to the following 8 ISGs: AXL receptor tyrosine kinase (AXL), interferon-alpha inducible protein 27 (IFI27), interferon-induced protein 44 (IFI44), interferon-induced protein 44-like (IFI44L), ISG15, OAS1, OAS3 and XIAP associated factor 1 (XAF1). It should be noted that the IFN-α2 and -ω microarray experiments were performed in different batches but batch effects were not corrected since genes were identified by the filtering approach just described within each batch.
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| Contributor(s) |
Wie S, Singhania A, Woelk CH |
| Citation(s) |
23276142 |
| Submission date |
Oct 19, 2012 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Akul Singhania |
| E-mail(s) |
akul.singhania@crick.ac.uk
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| Phone |
+442037963319
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| Organization name |
The Francis Crick Institute
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| Street address |
1 Midland Road
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| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL6884 |
Illumina HumanWG-6 v3.0 expression beadchip |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA178033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41731_4254964012.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_4254964024.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_4312191006.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_4312191012.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_4313143153.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_4313143154.sdf.gz |
3.3 Kb |
(ftp)(http) |
SDF |
| GSE41731_RAW.tar |
62.5 Mb |
(http)(custom) |
TAR (of IDAT) |
| GSE41731_non-normalized.txt.gz |
16.9 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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