Global mapping of the macrophage-HIV-1 transcriptome reveals that productive infection induces remodeling of the host cell DNA and chromatin [miRNA-seq]
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PROVIDER: PRJNA765596 | ENA |
REPOSITORIES: ENA
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Project description:It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. To shed light on this important issue, we performed comparative analyses of mRNA expression levels of host genes in uninfected bystander and HIV-1-infected human macrophages using an infectious reporter virus construct coupled with a large-scale RNA sequencing approach. We observed a rapid differential expression of several host factors in the productively infected macrophage population including genes regulating DNA replication factors and chromatin remodeling. A siRNA-mediated screening study to functionally identify host determinants involved in HIV-1 biology has provided new information on the virus molecular regulation in macrophages.
2021-07-21 | GSE180273 | GEO
Project description:Global mapping of the macrophage-HIV-1 transcriptome reveals that productive infection induces remodeling of the host cell DNA and chromatin
| PRJNA747301 | ENA
Project description:It has been proposed that macrophages could serve as long-lived compartments for HIV-1 infection under in vivo situations because these cells are resistant to the virus-mediated cytopathic effect, produce progeny virus over extended periods of time and are localized in tissues that are often less accessible by treatment. Comprehensive experimental studies are thus needed to characterize the HIV-1-induced modulation of host genes in these myeloid lineage cells. To shed light on this important issue, we performed comparative analyses of mRNA expression levels of host genes in uninfected bystander and HIV-1-infected human macrophages using an infectious reporter virus construct coupled with a large-scale RNA sequencing approach. We observed a rapid differential expression of several host factors in the productively infected macrophage population including genes regulating DNA replication factors and chromatin remodeling. A siRNA-mediated screening study to functionally identify host determinants involved in HIV-1 biology has provided new information on the virus molecular regulation in macrophages.
| S-EPMC5507862 | biostudies-other
Project description:This data corresponds to the microRNA expression profiles for the exact same samples from GSE180273.
2023-09-01 | GSE184665 | GEO
Project description:Aguilera 2014 - HIV latency. Interaction
between HIV proteins and immune response
This model is described in the article:
Studying HIV latency by
modeling the interaction between HIV proteins and the innate
immune response.
Aguilera LU,
Rodríguez-González J.
J. Theor. Biol. 2014 Nov; 360:
67-77
Abstract:
HIV infection leads to two cell fates, the viral productive
state or viral latency (a reversible non-productive state). HIV
latency is relevant because infected active CD4+ T-lymphocytes
can reach a resting memory state in which the provirus remains
silent for long periods of time. Despite experimental and
theoretical efforts, the causal molecular mechanisms
responsible for HIV latency are only partially understood.
Studies have determined that HIV latency is influenced by the
innate immune response carried out by cell restriction factors
that inhibit the postintegration steps in the virus replication
cycle. In this study, we present a mathematical study that
combines deterministic and stochastic approaches to analyze the
interactions between HIV proteins and the innate immune
response. Using wide ranges of parameter values, we observed
the following: (1) a phenomenological description of the viral
productive and latent cell phenotypes is obtained by bistable
and bimodal dynamics, (2) biochemical noise reduces the
probability that an infected cell adopts the latent state, (3)
the effects of the innate immune response enhance the HIV
latency state, (4) the conditions of the cell before infection
affect the latent phenotype, i.e., the existing expression of
cell restriction factors propitiates HIV latency, and existing
expression of HIV proteins reduces HIV latency.
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2024-09-02 | BIOMD0000000573 | BioModels
Project description:Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for HIV infection. Here, we implement a systems approach to discover molecular signatures of HIV latently-infected CD4+ T cells, identifying the immunosuppressive, adenosine-producing ectonucleotidase CD73 as a key surface marker of latent cells. Hypoxic conditioning, reflecting the lymphoid tissue microenvironment, increases the frequency of CD73+ CD4+ T cells and promotes HIV latency. Transcriptomic profiles of CD73+ CD4+ T cells favor viral quiescence, immune evasion, and cell survival. CD73+ CD4+ T cells are capable of harboring a functional HIV reservoir and reinitiating productive infection ex vivo. CD73 or adenosine receptor blockade facilitates latent HIV reactivation in vitro, mechanistically linking adenosine signaling to viral quiescence. Finally, tissue imaging of lymph nodes from HIV-infected individuals on antiretroviral therapy reveals spatial association between CD73 expression and HIV persistence in vivo. Our findings warrant development of HIV cure strategies targeting the hypoxia-CD73-adenosine axis.
2023-09-24 | GSE243577 | GEO
Project description:Deciphering the mechanisms underlying viral persistence is critical to achieving a cure for HIV infection. Here, we implement a systems approach to discover molecular signatures of HIV latently-infected CD4+ T cells, identifying the immunosuppressive, adenosine-producing ectonucleotidase CD73 as a key surface marker of latent cells. Hypoxic conditioning, reflecting the lymphoid tissue microenvironment, increases the frequency of CD73+ CD4+ T cells and promotes HIV latency. Transcriptomic profiles of CD73+ CD4+ T cells favor viral quiescence, immune evasion, and cell survival. CD73+ CD4+ T cells are capable of harboring a functional HIV reservoir and reinitiating productive infection ex vivo. CD73 or adenosine receptor blockade facilitates latent HIV reactivation in vitro, mechanistically linking adenosine signaling to viral quiescence. Finally, tissue imaging of lymph nodes from HIV-infected individuals on antiretroviral therapy reveals spatial association between CD73 expression and HIV persistence in vivo. Our findings warrant development of HIV cure strategies targeting the hypoxia-CD73-adenosine axis.
2023-09-28 | GSE244190 | GEO
Project description:HIV establishes long-term latent infection in memory CD4+ T cells, but also establishes sustained long-term productive infection in macrophages, especially in the CNS. To better understand how HIV sustains infection in macrophages, we performed RNAseq analysis after infection of human-monocyte derived macrophages (MDMs) with the brain-derived HIV-1 strain YU2 and compared this with acute infection of CD4+ T cells. HIV infection in MDM and CD4+ T-cells altered many gene transcripts, but with few overlaps between these different cell types. We found interferon pathways upregulated in both MDM and CD4+ T-cells, but with different gene signatures. The interferon-stimulated gene RSAD2/Viperin was among the most upregulated genes following HIV infection in MDMs, but not in CD4+ T-cells. RSAD2/Viperin was induced early after infection with various HIV strains, was sustained over time, and remained elevated in established MDM infection even if new rounds of infection were blocked by antiretroviral treatment. Immunofluorescence microscopy revealed that RSAD2/Viperin was induced strongly in HIV infected cells, as well as in some uninfected neighboring cells, and was frequently localized at junctions between cells. Knockdown of RSAD2/Viperin following establishment of infection in MDMs reduced production of HIV transcripts and viral p24 antigen. This correlated with reduction in the number of multinucleated giant cells, and changes in the histone modifications at the HIV LTR, including loss of histone H3K7ac and H3K9me3, epigenetic marks that we have found associated with HIV in MDMs. RNA-seq transcriptomic analysis of RSAD2/Viperin knockdown during HIV infection of MDMs revealed activation of interferon alpha and gamma pathways and inactivation of Rho GTPase pathways. Taken together, these results suggest that RSAD2/Viperin supports HIV infection in macrophages through multiple mechanisms, potentially including the attenuation of the interferon response.
2024-08-27 | GSE253073 | GEO
Project description:HIV-1 Tat protein is essential for virus production. RNA-binding proteins that facilitate Tat production may be absent or downregulated in resting CD4+ T-cells, the main reservoir of latent HIV. In this study, we examined the role of Tat RNA-binding proteins on the expression of Tat and control of latent and productive infection.
2021-06-14 | PXD025782 | Pride
Project description:BET proteins commonly activate cellular gene expression, yet inhibiting their recruitment paradoxically reactivates latent HIV-1 transcription. Here we identify the short isoform of BET family member BRD4 (BRD4S) as a novel corepressor of HIV-1 transcription. We found that BRD4S was enriched in chromatin fractions of latently infected T cells and was more rapidly displaced from chromatin upon BET inhibition than the long isoform. BET inhibition induced marked nucleosome remodeling at the latent HIV-1 promoter, which was dependent on the activity of BAF, a SWI/SNF chromatin-remodeling complex with known repressive functions in HIV-1 transcription. BRD4S directly bound BRG1, a catalytic subunit of BAF, via its bromo- and ET domains and was necessary for BRG1 recruitment to latent HIV-1 chromatin. Using ChIP-seq combined with ATAC-seq data, we found that the latent HIV-1 promoter phenotypically resembles endogenous LTR sequences, pointing to a select role of BRD4S:BRG1 complexes in genomic silencing of invasive retroelements.
2017-08-21 | GSE100266 | GEO