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Comparative DNA methylomic analyses reveal insight into potential origins of novel monocyte epigenetic biomarkers of insulin resistance

ABSTRACT: Genome wide DNA methylation profiling of monocytes from insulin sensitive and insulin resistant HIV-infected patients. The Illumina Infinium Human Methylation 450k Beadchip was used to obtain DNA methylation profiling across 450,000+ CpGs. Samples included monocytes from 37 HIV-infected individuals, of which 14 were insulin resistant and 23 were insulin sensitive, monocytes from 9 HIV-seronegative individuals, of which 4 were insulin sensitive and 5 insulin resistant, and FACS monocyte subsets (classical, intermediate, and non-classical monocytes) from two healthy donors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE131627 | GEO | 2019/06/25

REPOSITORIES: GEO

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Interferon alpha-inducible protein 27 (IFI27) expression is linked to disease severity in chronic infection of both HIV-1 and HIV-2

Project description:To explore if specific host responses are linked to HIV disease severity, we here investigated blood gene expression profiles comparing different progressor groups, including those with HIV-1, HIV-2 or HIV-1/HIV-2 dual infection and HIV seronegative individuals. We found interferon alpha-inducible protein 27 (IFI27) to be the most strongly, and significantly, upregulated gene in HIV infected, compared with HIV seronegative, individuals. The expression of IFI27 was higher in HIV-1, compared with HIV-2, infected individuals and correlated with both plasma viral load (pVL) and CD4% levels.

2022-05-31 | GSE200606 | GEO

MicroRNA regulation and its effects on cellular transcriptome in Human Immnodeficiency Virus-1 (type-1) infected individuals with distinct viral load and CD4 cells

Project description:Human PBMCs were isolated from donors' blood. We used Taqman low density arrays to examine the differences in microRNA expression in the PBMCs of HIV seronegative individuals and individuals infected with low and high viral load.

2015-04-01 | GSE46018 | GEO

Transcription profiling of human peripheral blood mononuclear cells infected with HIV-1

Project description:We used Affymetix HG Focus GeneChip to measure the expression levels of HIV seronegative and seropositive individuals in human PBMCs in vivo. GSM39104 -GSM39115 are HIV seronegative samples; GSM39116-GSM39137 are HIV seropositive but drug naive samples; GSM39138-GSM39147 are HIV seropositive samples used to test serostatus biomarker; GSM39148-GSM39170 are HIV seropositive individuals whose CD4 cells decrease over time; GSM39171-GSM39187 are HIV seropositive individuals whose CD4 cells increase over time; GSM39188-GSM39190 are HIV seropositive samples used to test CD4 cell increase/decrease over time.

2007-08-25 | E-GEOD-2171 | biostudies-arrayexpress

MicroRNA regulation and its effects on cellular transcriptome in Human Immnodeficiency Virus-1 (type-1) infected individuals with distinct viral load and CD4 cells

2015-04-01 | E-GEOD-46018 | biostudies-arrayexpress

HIV-1 infection in human PBMCs in vivo

2005-01-22 | GSE2171 | GEO

Epigenome analysis in several cohorts of HIV progession and in uninfected individuals

Project description:Genome wide DNA methylation profiling of CD4 T cells from uninfected and HIV-infected individuals (viremic, ART-suppressed and elite controllers [EC]) The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,577 CpGs in DNA from peripheral CD4 T cells samples. Samples included: 22 from HIV-uninfected individuals (uninfected group), 42 from HIV-infected individuals (21 from HIV-infected viremic (viremic group) and 21 from the same participants after viral suppression (viral load< 50 copies HIV-1 RNA/plasma) by antiretroviral therapy administrarion (ART group), and 21 from elite controllers (EC group)

2023-01-16 | GSE143942 | GEO

Blood plasma from people living with HIV-1 or HIV-2

Project description:In this study we performed data-independet mass-spectrometry analysis of blood plasma collected from a cohort consisting of people living with HIV-1, people living with HIV-2, and HIV seronegative individuals. The data was used to infer signs of damage to a wide array of tissues and cell types.

2024-02-16 | PXD045155 | Pride

IFN-a-induced monocyte phenotype in chronic unsuppressed HIV infection

Project description:Abstract Objectives: HIV infection dysregulates the innate immune system and alters leukocyte gene expression. The objectives were two fold: to characterize the impact of HIV infection on peripheral monocyte gene expression and to identify the predominant factor(s) responsible for altered gene expression. Design and methods: In a cross-sectional study, CD14+ monocytes were isolated from 11 HIV seronegative controls, 22 HIV seropositive subjects with low viral loads (LVL, <= 10,000 RNA copies/ml) and 22 HIV seropositive subjects with high viral loads (HVL, > 10,000 RNA/copies/ml). Total monocyte RNA was hybridized to 55K probes on high-density microarrays to obtained detailed gene expression profiles from control, LVL and HVL subjects. As potential candidates for immune disruption, we evaluated three HIV-related peripheral factors, interferon (IFN)-a, IFN-a and lipopolysaccharide (LPS) by treating HIV seronegative CD14+ monocytes for 48h and then analyzing gene expression. Plasma collected from the HIV subjects were quantified for LPS using a Pyrogene assay and for soluble (s) CD14 by ELISA. Results: In this cross-sectional study of HIV subjects (n=44), viral loads above 10,000 RNA copies/ml were associated with an activated phenotype. Characterization of the gene expression pattern by Gene Ontology reveals an ongoing immune response to viral infection including inflammation and chemotaxis. Gene expression analysis of in vitro treated HIV seronegative monocytes with IFN-a, IFN-g or LPS demonstrated that IFN-a most accurately recapitulated the HIV HVL profile. There was no detectable LPS signature even in those HIV subjects with the highest LPS and sCD14 levels. Conclusions: Monocyte gene expression in subjects with viremia is predominantly due to IFN-a, while subjects with LVL have a non-activated phenotype. In monocytes, there was no discernible expression profile linked to LPS exposure.

2009-10-09 | GSE18464 | GEO

Epigenome-wide assoication analysis of HIV infection

Project description:Genome wide DNA methylation profiling of HIV-infected and uninfected individuals for DNA samples extracted from peripheral blood. The Illumina Infinium Human DNA methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Samples included 261 HIV-infected and 117 HIV-uninfected individuals. The goal was to identify genome-wide differentially methylated CpG sites between HIV-infected and uninfected samples. Bisulfite converted DNA from the 378 DNA samples were hybridized to the Illumina Infinium 450K Human Methylation Beadchip. The samples were extracted from whole blood. The subjects including 261 HIV-infected and 117 HIV-uninfected were recruited from the Veteran Aging Cohort Study. All subjects were inform consented and the study protocol was approved by Connecticut Veteran Affair Healthcare System IRB and Yale Human Research Protection Program at Yale University.

2017-02-09 | GSE77696 | GEO

Complementation can maintain a quasispecies of drug sensitive and resistant HIV

Project description:The goal of this study was to determine how an HIV quasispecies is maintained in the face of selection. We deep sequenced the HIV provirus from cell populations as well as single cells at different time points from in vitro evolution experiments and found that when a less fit and more fit infect the same cell, they share components (complmentation) and therefore allow the less fit to perpetuate. We reproduced a quasispecies to an HIV reverse transcriptase inhibitor. The drug resistant genotype never completely supplanted the drug sensitive genotype, which stabilized at about 20% of viral sequences. Single-cell sequencing showed that resistant genotype frequency plateaued when cells were co-infected with sensitive and resistant genotypes, suggesting a sharing of viral proteins in co-infected cells (complementation), masking genotypic differences. To test if complementation can confer phenotypic drug resistance, we co-transfected fluorescently labelled molecular clones of sensitive and resistant HIV and observed drug resistance in genotypically sensitive virus from co-transfected cells. Resistant virus preferentially co-infected cells with drug sensitive HIV, explaining initiation of co-infections. Modelling showed that a stable quasispecies could form at the experimental multiplicities of infection. Conclusions: Complementation can lead to a quasispecies in infection environments where multiple infections per cell are common

2020-05-13 | GSE150390 | GEO

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