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Citation: Songok EM, Luo M, Liang B, Mclaren P, Kaefer N, Apidi W, et al. (2012) Microarray Analysis of HIV Resistant Female Sex Workers Reveal a Gene Expression Signature Pattern Reminiscent of a Lowered Immune Activation State. PLoS ONE 7(1): e30048. https://doi.org/10.1371/journal.pone.0030048.
Editor: Clive M. Gray, University of Cape Town, South Africa.
Received: May 17, 2011; Accepted: December 8, 2011; Published: January 26, 2012.
Copyright: © 2012 Songok et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was funded by Bill and Melinda Gates Foundation under Grand Challenges in Global Health (GCGH) initiative and the Canada Institutes of Health Research (CIHR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
The disease AIDS perhaps ranks as one of the most devastating scourges of mankind. Since it was identified in 1983 more than 30 million people have died and another 33 million currently live with the virus [1], [2]. The majority of HIV-1 infections occur in Sub-Saharan Africa, where in some countries prevalence rates of more than 40% have been documented among antenatal clinic attendees [3]. Despite advances made in antiretroviral therapy, only a third of those requiring treatment receive it and new infections far outstrip those on therapy [4]. Similar to other previous viral epidemics, prevention through vaccination shall be the best approach. However, the nature of the AIDS virus to integrate itself to the host genome and its ability to constantly mutate and shield immunogenic components that induce protective antibodies, continue to pose challenges for an effective vaccine. Though a recent prime boost vaccine strategy, RV 144, provided signals that a HIV-1 vaccine was possible, its efficacy was only a modest 30% [5].
The presence of individuals who are highly exposed to HIV-1 but do not get infected, provide hope for a better understanding of correlates for protection that may lead to a more effective vaccine strategy. Highly exposed seronegative (HESN) populations have been identified among intravenous drug users [6], children born to seropositive mothers [7], [8], discordant couples [9], [10], and commercial sex workers [11]–[13]. The findings in 1996 on the protective effect of the CCR5?32 allele in HIV-1 infection [14] shifted focus to host genetics as probable cause of HIV-1 resistance. Over the past 10 years, approximately 40 genes have been documented from HESN populations as possible candidates for differential host susceptibility to HIV-1 [15]. This include selected human leukocyte antigens, HLA [16], TRIM5? [17], specific KIR-HLA associations [18], and APOBEC3G [19]. However, only a fraction of HESN has the protective genotypes described in the literature. Previous gene discovery studies have focused on single gene approaches which may have missed other compelling gene candidates and overlook interactions between different genes or genetic pathways. Microarray expression profiling provides new opportunities for simultaneous analysis of thousands of messenger RNA expression patterns in tandem with their biological functions. Less data exist on the use of microarrays to identify biomarkers for HIV-1 susceptibility, including pathways that may be critical for successful anti-HIV-1 vaccine and therapeutic design. In a bid to determine biomarkers and genetic pathways that are unique to HESNs, we carried out a global whole blood gene expression profiling of HIV-1 highly exposed and uninfected individuals from a well-characterized female commercial sex worker cohort from Nairobi, Kenya.
Gene expression outcome.
Our primary objective was to investigate if there is a predictive gene expression pattern that defines the HESN phenotype. Gene expression data from the 86 micro arrays were normalized and all were included in the analysis. An unsupervised hierarchical clustering algorithm was run on the data to ascertain if the two populations could be separated into two distinct groups based on their gene expression profiles. Figure 1 show a distinct separation between the HESN (Test) and HIV negative controls (Controls).
Each row on the Y axis represents a single gene probe and the phylograms represent distinct signaling pathways. The red color denotes up regulated genes while the green are down regulated.
Of the 54675 gene probe sets represented on the Affymetrix U133 plus 2.0 gene chip, 2,274 probe sets were differentially expressed in the HESN group as compared with the control group (fold change ?1.3; p value ?0.05) after correction with multiple testing using the Benjamin-Hochberg false discovery rate (FDR<0.05). Of the total differentially expressed transcripts, 462 (20%) could be mapped onto the KEGG signaling database. Figure 2 shows the 15 signaling events with the highest number of genes identified through the KEGG analysis. Majority of these pathways (13 of 15, 87%) were significantly down-regulated in the HESN group. The top ranked down-regulated pathways belonged to energy metabolism, cell adhesion, signal transduction and immune signaling categories. Glucose/gluconeogenesis and pentose phosphate phosphorylation (p<0.0003) were the most down-regulated metabolic pathways, together with the immune signaling events of natural killer cell cytotoxicity (p<0.008), antigen processing and presentation (p<0.0013) and T-cell receptor signaling. The key up-regulated pathways were the ribosome protein synthesis and tight junction. Figures 3 (a to g) show the heatmaps of representative genes in the significantly impacted pathways. Gene ontology (GO) classification of the differentially expressed transcripts identified protein binding as the major functional group among the down-regulated genes (Fig. 4a). In contrast, up-regulated genes were significantly associated with nuclear binding (Fig. 4b).

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