Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide DNA methylation analysis reveals dynamic changes in metabolic and immune-regulatory pathways during uncontrolled SIV infection

ABSTRACT: The molecular mechanisms underlying HIV-induced inflammation remain incompletely defined although they associate with morbidity and progression to AIDS. Here we used non-human primate models of pathogenic and nonpathogenic simian immunodeficiency virus (SIV) infection in respectively macaques and African green monkeys. We longitudinally analyzed DNA methylation changes in CD4+ T cells from lymph node and blood using species-compatible probes on human 450K methylation BeadArrays. Selected identified sites were validated using bisulfite-pyrosequencing of an independent cohort of uninfected, viremic and SIV controller macaques. Tissue- and species-specific DNA methylation changes were observed after SIV infection. The most affected genes in pathogenic SIV infection were related to metabolic pathways and Th1 signaling. SIV-infected macaques displayed increased insulin sensitivity early in the chronic phase of infection, which correlated with T cell activation. Moreover, DNA methylation changes in the Th1 pathway were associated with altered gene expression. Out of the 11 selected genes for validation, six genes showed differential methylation in viremic and uninfected macaques. In contrast, no significant differences were found between uninfected and SIV-controller macaques. In summary, pathogenic SIV infection associates with DNA methylation changes in genes related to metabolism and immune-regulation.

ORGANISM(S): Homo sapiens Chlorocebus sabaeus Macaca mulatta

PROVIDER: GSE143708 | GEO | 2020/12/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression data from rhesus macaque blood CD8+ T cells

Project description:Immunization of macaques with simian immunodeficiency virus with deletions in nef (SIV?nef) has been shown to elicit protective immunity to infection by pathogenic SIV, yet our understanding of the mechanisms that orchestrate protection and prevent pathogenesis remains limited. In the study, we utilize whole-genome transcriptional profiling to reveal molecular signatures of protective immunity in circulating CD8+ T cells of rhesus macaques vaccinated with SIVmac239?nef and challenged with pathogenic SIVmac251. Microarrays were used to characterize changes in gene expression in blood CD8+ T cells that occur following vaccination of rhesus macaques with attenuated SIV?nef and subsequent challenge with pathogenic SIVmac251, in comparison to corresponding changes in healthy controls and unvaccinated animals infected with pathogenic SIVmac251 CD8+ T cells were isolated by magnetic beads from the blood of healthy uninfected macaques, macaques vaccinated with SIV?nef, and unvaccinated controls infected with SIVmac251, and used for RNA extraction and hybridization on Affymetrix microarrays. Blood samples from vaccinated animals were collected prior to vaccination, at 3, 20, and 40 weeks following vaccination. After the 40 week vaccination period, macaques were challenged with SIVmac251, and blood was again collected at 3 weeks following challenge. Blood was collected from the unvaccinated controls at 3 weeks following infection with SIVmac251

2014-09-26 | E-GEOD-61766 | biostudies-arrayexpress

Gene Expression Analysis of Host Immune Responses in rhesus macaques infected with SIVmac239 or deglycosylated live-attenuated SIV

Project description:To find the differences in innate immune response between nonpathogenic and pathogenic SIV infection, we examined transcriptome in PBMCs from macaques infected with pathogenic or nonpathogenic SIV.

2014-10-10 | GSE62209 | GEO

Expression data from rhesus macaque tongue

Project description:A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. Microarrays were used to characterize changes in gene expression in the tongue mucosa that occur during chronic SIV infection. Dorsal tongue tissues from healthy uninfected macaques and macaques with chronic stage SIV infection were used for RNA extraction and hybridization on Affymetrix microarrays.

2014-01-01 | E-GEOD-51436 | biostudies-arrayexpress

gut metagenome

Project description:Experimental Colitis in SIV-uninfected Rhesus Macaques Recapitulates Key Features of Pathogenic SIV Infection

| PRJNA288157 | ENA

Expression data from rhesus macaque colon, jejunum, and lung

Project description:The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy. Microarrays were used to characterize changes in gene expression in the colonic, jejunal, and pulmonary (lung) mucosa that occur during chronic SIV infection in the presence or absence of antiretroviral therapy. Colon, jejunum, and lung tissues from healthy uninfected macaques and macaques with chronic stage SIV infection (+/- therapy) were used for RNA extraction and hybridization on Affymetrix microarrays.

2013-11-01 | E-GEOD-51615 | biostudies-arrayexpress

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

Expression data from rhesus macaque tongue epithelium

Project description:A majority of individuals infected with human immunodeficiency virus (HIV) have inadequate access to antiretroviral therapy and ultimately develop debilitating oral infections that often correlate with disease progression. Our study evaluates the potential of simian immunodeficiency virus (SIV) infected rhesus macaques to serve as a non-human primate model for oral manifestations of HIV disease. Microarrays were used to characterize changes in gene expression in the dorsal tongue epithelium that occur during chronic SIV infection. Epithelial cells were laser microdissected from dorsal tongue tissue sections from healthy uninfected macaques and macaques with chronic stage SIV infection and used for RNA extraction and hybridization on Affymetrix microarrays.

2014-01-01 | E-GEOD-51438 | biostudies-arrayexpress

Gene expression in the blood of Live Attenuated Rev-Independent NefÂ¯SIV infected Rhesus macaques during acute infection

Project description:Rhesus macaques (RMs) inoculated with live-attenuated Rev-Independent NefÂ¯ simian immunodeficiency virus (Rev-Ind NefÂ¯SIV) as adults or neonates controlled viremia to undetectable levels and showed no signs of immunodeficiency over 6-8 years of follow-up. We tested the capacity of this live-attenuated virus to protect RMs against pathogenic, heterologous SIVsmE660 challenges Blood PBMC Time after SIV infection: 2 weeks post SIV infection Infection:Rev-Ind NefÂ¯SIV

2013-08-09 | E-GEOD-49663 | biostudies-arrayexpress

Rapid SIV Env-specific mucosal and serum antibody induction augments cellular immunity in protecting immunized, elite-controller macaques against high dose heterologous SIV challenge

Project description:Goal of this study was to assess the levels of protection and investigate cellular, humoral, and mucosal immune correlates on the functional and gene transcriptional levels in elite-controller macaques following high dose SIV challenge. Three experimental, post SIV smE660 challenge macaque jejunal samples were individually compared to four pre SIV smE660 challenge baseline samples.

2010-08-23 | E-GEOD-23722 | biostudies-arrayexpress

Gene Expression Analysis of Host Immune Responses in rhesus macaques infected with SIVmac239 or deglycosylated live-attenuated SIV

Project description:To find the differences in innate immune response between nonpathogenic and pathogenic SIV infection, we examined transcriptome in PBMCs from macques infected with pathogenic or nonpathogenic SIV. Juvenile macaques were intavenousy infected with SIVmac239 or M-bM-^HM-^F5G. Blood samples were collected at 1 week and 3 weeks pi. Total RNA from the PBMCs were used for the microarray analysis.

2014-10-10 | E-GEOD-62209 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data