NanoString miRNA profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors
ABSTRACT: This study used the NanoString nCounter hybridization system and nCounter miRNA expression assays to identify and quantitate circulating cellular miRNAs during HIV-1 elite suppression, active HIV-1 replication, and uninfected status. Overall design: Blood samples were from eight uninfected controls, seven HIV-1 elite suppressors with undetectable viral load, and six viremic HIV-1-infected patients.
INSTRUMENT(S): NanoString nCounter Human miRNA assay
Project description:This study used the NanoString nCounter hybridization system and nCounter miRNA expression assays to identify and quantitate circulating cellular miRNAs during HIV-1 elite suppression, active HIV-1 replication, and uninfected status. Blood samples were from eight uninfected controls, seven HIV-1 elite suppressors with undetectable viral load, and six viremic HIV-1-infected patients.
Project description:This study used TaqMan low-density arrays to identify and quantitate circulating cellular miRNAs during HIV-1 elite suppression, active HIV-1 replication, and uninfected status. Blood samples were from six uninfected controls, six HIV-1 elite suppressors with undetectable viral load, and six viremic HIV-1-infected patients.
Project description:This SuperSeries is composed of the following subset Series: GSE33387: NanoString miRNA profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors GSE33492: TaqMan Peripheral blood mononuclear cell miRNA profiles of HIV-1-infected elite suppressors, viremic patients, and uninfected control donors Refer to individual Series
Project description: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 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<200cp/ml) and 5 uninfected individuals (HIV-) through TaqMan® Array Human microRNA Cards v3.0. A differential expression pattern consisting of 23 miRNAs overcame 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. Peripheral blood mononuclear cell samples were from five uninfected controls, eight viremic HIV-1-infected patients, eight HIV-1 elite controllers with undetectable viral load and eight HIV-1antiretroviral treated individuals with undetectable viral load.
Project description:Elite Long-Term Nonprogressors are asymptomatic HIV-infected individuals who display long-term virtually undetectable viremia, stable CD4 T cell counts and extremeley low levels of HIV reservoir, in the absence of antiretroviral therapy. We conducted a whole-genome transcriptional profiling study of sorted resting CD4 T cell subsets (naive, central memory, transitional memory and effector memory) in 7 Elite Long-Term Nonprogressors, 7 HIV-infected viremic and 7 uninfected individuals. HIV-1 cellular DNA levels were quantified in each sorted CD4 T cell subset
Project description:Elite controllers maintain HIV-1 viral loads below the limit of detection. The mechanisms responsible for this phenomenon are poorly understood. As microRNAs (miRNAs) are regulators of gene expression and some of them modulate HIV infection, we have studied the miRNA profile in plasma from HIV elite controllers and chronically infected individuals and compared against healthy donors. Several miRNAs correlate with CD4+ T cell count or with the known time of infection. No significant differences were observed between elite controllers and healthy donors; however, 16 miRNAs were different in the plasma of chronic infected versus healthy donors. In addition, levels of hsa-miR-29b-3p, hsa-miR-33a-5p and hsa-miR-146a-5p were higher in plasma from elite controllers than chronic infected and hsa-miR-29b-3p and hsa-miR-33a-5p overexpression significantly reduced the viral production in MT2 cells. Therefore, levels of circulating miRNAs might be of diagnostic and/or prognostic value for HIV infection. Additionally, hsa-miR-29b-3p and miR-33a-5p may be used in therapeutic strategies. An exploratory cross-sectional study of microRNA levels in EDTA plasma samples. Plasma samples were obtained from 24 subjects and were classified in 3 groups, 9 Elite Controllers (defined as individuals with plasma viral load (PVL) < 50 copies/ml, CD4 count >350/ml), 9 chronic HIV patients (CH) under anti-retroviral treatment and 6 healthy HIV negative donors (HD). This study was approved by the Huésped Foundation Ethics Committee and informed consent was obtained from all subjects.
Project description:The relationship between host microRNAs (miRNA), viral control and immune response has not been elucidated in the field of HIV yet. The aim of this study was to assess the differential miRNA profile in CD8+ T-cells between HIV-infected individuals who differ in terms of disease progression. A total of 136 RNAs (miRNAs) were analyzed: 68 RNAs from resting CD8+ T-cells and the respective 68 RNAs from stimulated CD8+ T-cells from Elite Controllers (EC, n=15), Viremic Controllers (VC, n=15), Viremic Progressors (VP, n=13), Treated Patients (ART, n=14) and Uninfect Donors (HIV-, n=11).
Project description:Background: Prior analyses of mRNA expression in intestinal tissue as related to HIV cohorts has been on whole biopsies. More targeted isolation and enrichment of intestinal epithelial cells is needed to identify pathways specifically altered in the epithelium that may not be picked up at a global tissue scale. Results: Analysis of intestinal epithelial cells isolated from primary human tissues taken from HIV-infected cohorts as well as uninfected controls. Results demonstrate key genes differentially expressed in HIV in the absence or presence of ART-therapy. Overall design: Cross-sectional sampling and comparison of epithelial isolates from 9 uninfected, 6 viremic untreated, and 19 HIV-infected ART-treated patients. Whole biopsy RNA from 5 uninfected, 6 viremic untreated, and 5 HIV-infected ART-treated patients.
Project description:Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-Seq to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. We discover a highly functional antiviral DC state in ECs whose fractional abundance after in vitro exposure to HIV-1 correlates with higher CD4+ T cell counts and lower HIV-1 viral loads, and that effectively primes polyfunctional T cell responses in vitro. We identify and validate select immunomodulators that increase the fractional abundance of this state in primary peripheral blood mononuclear cells (PBMCs) from healthy individuals in vitro. Overall design: Single-cell RNA-seq profiling of HIV-1-exposed cDCs and media controls from 3 elite controllers used to identify reproducible gene expression programs associated with cell-intrinsic HIV-1 immune recognition.
Project description:There is great interindividual variability in HIV-1 viral set point after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene expression to viral control, and to relate it to genomic DNA polymorphism. RNA was extracted from purified CD4+ T-cells from 137 HIV-1 seroconverters, 16 elite controllers, and 3 healthy blood donors. Expression levels of more than 48,000 mRNA transcripts were assessed by the Human-6 v3 Expression BeadChips (Illumina). Genome-wide SNP data was generated from genomic DNA using the HumanHap550 Genotyping BeadChip (Illumina). We observed two distinct profiles with 260 genes differentially expressed depending on HIV-1 viral load. There was significant upregulation of expression of interferon stimulated genes with increasing viral load, including genes of the intrinsic antiretroviral defense. Upon successful antiretroviral treatment, the transcriptome profile of previously viremic individuals reverted to a pattern comparable to that of elite controllers and of uninfected individuals. Genome-wide evaluation of cis-acting SNPs identified genetic variants modulating expression of 190 genes. Those were compared to the genes whose expression was found associated with viral load: expression of one interferon stimulated gene, OAS1, was found to be regulated by a SNP (rs3177979, p=4.9E-12); however, we could not detect an independent association of the SNP with viral set point. Thus, this study represents the first attempt to integrate genome-wide SNP signals with genome-wide expression profiles in the search for biological correlates of HIV-1 control. It underscores the paradox of the association between increasing levels of viral load and greater expression of antiviral defense pathways. It also shows that elite controllers do not have a distinctive mRNA expression pattern in CD4+ T cells. Changes in RNA expression reflect responses to viral replication rather than a mechanism that might explain viral control Overall design: Total RNA from 202 samples obtained from CD4 T cells from HIV infected individuals to identify associations between variation in gene expression viral set point. Samples belong to different groups as follows (Paired Untreated/treated samples: 38/38, only untreated samples: 89, successfully treated samples: 29. Eight samples from 3 healthy blood donors in replicates.