Differential microRNA expression profile between stimulated PBMCs from HIV-1 infected elite controllers and viremic progressors

Abstract

Background: The emerging relationship between microRNAs (miRNA) and viral-control is a topic of interest in the field of HIV. Host-genome might play an important role in the control of viremia. The aim of this study was to assess the specific miRNA profile that could contribute to the control of HIV replication in Elite Controllers.

Results: After adequate normalization, expression profile of 286 human miRNAs (hsa-miR) was evaluated in phytohaemagglutinin-stimulated PBMCs from 29 individuals classified in 4 groups: 8 elite controllers (EC; viral load <50 cp/ml without treatment), 8 viremic progressors (VP; VL>5000 cp/ml without treatment), 8 patients under antiretroviral treatment (ART; VL<200 cp/ml) and 5 uninfected individuals (HIV-) through TaqMan Array Human microRNA Cards v3.0. A differential expression pattern consisting of 23 miRNAs became significantly different when comparing EC and VP. Profiling analysis segregated the population in two different blocks: while EC and HIV- clustered together in the same block (EC/HIV-_block 1), VP and ART individuals clustered together in a second block (VP/ART_block 2). Two inversely expressed miRNA patterns were determined within those two blocks: a set of 4 miRNAs (hsa-miR-221, -27a, -27b and -29b) was up-expressed in EC/HIV-_block and down-expressed in VP/ART_block while 19 miRNAs were down-expressed in block 1 and up-expressed in block 2. Differential miRNAs were successfully validated through individual RT-qPCR assays.

Conclusions: Profile in EC resembled HIV- and differentially clusters with VP and ART. Therefore, differential clustering does not rely on undetectable viremia.

Figure 1. Differential miRNAs between Elite Controllers (EC) and Viremic Progressors (VP).

A) Hierarchical clustering of the differentially expressed miRNAs between EC and VP. Patients are ordered on vertical lines and candidate miRNAs on horizontal lines. For each miRNA, green represents under-expressed and red over-expressed values compared to the average value (median), in dark. Dendrograms (tree graph) between patients and between miRNAs are depicted, where the closest branches of the tree represent patients/miRNAs with the most similar expression pattern. Two blocks of patients (Block 1/Block 2) with an inverse expression profile were segregated. Two groups of miRNAs (Group 1/Group 2) with an inverse expression profile were segregated within each block. B) Fold change (log 2) of the 23 differentially expressed miRNAs in EC. Differential levels are normalized to all assesed miRNAs and relative to VP. Bars represent standard error means (SEM).

Figure 2. Fold change (log₂) of the 23 differentially expressed miRNAs in EC and VP.

A) normalized to all assessed miRNAs and relative to ART, B) normalized to all assessed miRNAs and relative to HIV-. Bars represent standard error means (SEM); *, p<0.05; **, p<0.01; ***, p<0.001; VP, viremic progressors; EC, elite controllers; ART, antiretroviral therapy.

Figure 3. Fold change (log₂) of EC, VP and ART, normalized to endogenous control miRNAs and relative to HIV-.

One-way analysis of variance (ANOVA) tests were performed for global comparisons and Turkey post-hoc tests for pair comparisons. Bars represent standard error means (SEM); *, p<0.05; **, p<0.01; ***, p<0.001 for Tuckey post-hoc tests; VP, viremic progressors; EC, elite controllers; ART, antiretroviral therapy.