Title |
Microarray Analysis of HIV Resistant Female Sex Workers Reveal a Gene Expression Signature Pattern Reminiscent of a Lowered Immune Activation State
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Published in |
PLOS ONE, January 2012
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DOI | 10.1371/journal.pone.0030048 |
Pubmed ID | |
Authors |
Elijah M. Songok, Ma Luo, Ben Liang, Paul Mclaren, Nadine Kaefer, Winnie Apidi, Genevieve Boucher, Joshua Kimani, Charles Wachihi, Rafick Sekaly, Keith Fowke, Blake T. Ball, Francis A. Plummer |
Abstract |
To identify novel biomarkers for HIV-1 resistance, including pathways that may be critical in anti-HIV-1 vaccine design, we carried out a gene expression analysis on blood samples obtained from HIV-1 highly exposed seronegatives (HESN) from a commercial sex worker cohort in Nairobi and compared their profiles to HIV-1 negative controls. Whole blood samples were collected from 43 HIV-1 resistant sex workers and a similar number of controls. Total RNA was extracted and hybridized to the Affymetrix HUG 133 Plus 2.0 micro arrays (Affymetrix, Santa Clara CA). Output data was analysed through ArrayAssist software (Agilent, San Jose CA). More than 2,274 probe sets were differentially expressed in the HESN as compared to the control group (fold change ≥1.3; p value ≤0.0001, FDR <0.05). Unsupervised hierarchical clustering of the differentially expressed genes readily distinguished HESNs from controls. Pathway analysis through the KEGG signaling database revealed a majority of the impacted pathways (13 of 15, 87%) had genes that were significantly down regulated. The most down expressed pathways were glycolysis/gluconeogenesis, pentose phosphate, phosphatidyl inositol, natural killer cell cytotoxicity and T-cell receptor signaling. Ribosomal protein synthesis and tight junction genes were up regulated. We infer that the hallmark of HIV-1 resistance is down regulation of genes in key signaling pathways that HIV-1 depends on for infection. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Iran, Islamic Republic of | 1 | 33% |
Unknown | 2 | 67% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 2 | 67% |
Practitioners (doctors, other healthcare professionals) | 1 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Germany | 1 | 1% |
Kenya | 1 | 1% |
Brazil | 1 | 1% |
India | 1 | 1% |
Spain | 1 | 1% |
United States | 1 | 1% |
Unknown | 80 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 18 | 21% |
Student > Ph. D. Student | 13 | 15% |
Student > Master | 12 | 14% |
Student > Bachelor | 10 | 12% |
Professor > Associate Professor | 8 | 9% |
Other | 15 | 17% |
Unknown | 10 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 27 | 31% |
Medicine and Dentistry | 26 | 30% |
Immunology and Microbiology | 11 | 13% |
Biochemistry, Genetics and Molecular Biology | 5 | 6% |
Social Sciences | 3 | 3% |
Other | 5 | 6% |
Unknown | 9 | 10% |