title: Microarray analysis of HIV resistant female sex workers reveal a gene expression signature pattern reminiscent of a lowered immune activation state.
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.
authors.affiliation: Kenya Medical Research Institute, Nairobi, Kenya. Esongok@kemri.org
authors.forename: Elijah M
authors.initials: EM
authors.lastname: Songok
authors.forename: Ma
authors.initials: M
authors.lastname: Luo
authors.forename: Ben
authors.initials: B
authors.lastname: Liang
authors.forename: Paul
authors.initials: P
authors.lastname: Mclaren
authors.forename: Nadine
authors.initials: N
authors.lastname: Kaefer
authors.forename: Winnie
authors.initials: W
authors.lastname: Apidi
authors.forename: Genevieve
authors.initials: G
authors.lastname: Boucher
authors.forename: Joshua
authors.initials: J
authors.lastname: Kimani
authors.forename: Charles
authors.initials: C
authors.lastname: Wachihi
authors.forename: Rafick
authors.initials: R
authors.lastname: Sekaly
authors.forename: Keith
authors.initials: K
authors.lastname: Fowke
authors.forename: Blake T
authors.initials: BT
authors.lastname: Ball
authors.forename: Francis A
authors.initials: FA
authors.lastname: Plummer
mesh_terms: D016000:Cluster Analysis; D015331:Cohort Studies; D015536:Down-Regulation / Q000235:genetics / Q000276:immunology; D005260:Female; D020869:Gene Expression Profiling; D015658:HIV Infections / Q000235:genetics / Q000276:immunology*; D015497:HIV-1 / Q000276:immunology*; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics*; D007630:Kenya; D008213:Lymphocyte Activation / Q000235:genetics* / Q000276:immunology; D046228:Microarray Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D060386:Sex Workers; D054928:Validation Studies as Topic