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HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [miRNA]

ABSTRACT: HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [miRNA]

PROVIDER: PRJNA505884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8203920.fastq.gz	Fastqsanger.gz
	SRR8203930.fastq.gz	Fastqsanger.gz
	SRR8203940.fastq.gz	Fastqsanger.gz
	SRR8203921.fastq.gz	Fastqsanger.gz
	SRR8203931.fastq.gz	Fastqsanger.gz

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HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture

Project description:HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture

| PRJNA505882 | ENA

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [miRNA]

Project description:Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells Results: Differences in a set of microRNAs Conclusions: Nef-transfection induces changes in the microRNA content of exosomes

2018-11-18 | GSE122656 | GEO

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [mRNA]

Project description:Purpose: Comparison of RNA-sequencing datasets obtained from exosomes of Nef-transfected and Mock-transfected HEK293T cells. Methods: Assessment of RNA content of exosomes produced by Nef-transfected HEK293T cells and and Mock-transfected HEK293T cells. Results: Differences in a set of mRNAs. Conclusions: Nef-transfection might induces changes in the mRNA content of exosomes.

2018-11-18 | GSE122655 | GEO

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [mRNA]

Project description:HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture [mRNA]

| PRJNA505883 | ENA

HIV Nef transfected HEK293T cell culture and HIV mock transfected HEK293T cell culture

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-11-18 | GSE122657 | GEO

HIV-1 Nef changes the proteome of T cells extracellular vesicles

Project description:Extracellular vesicles (EVs) are biomolecule carriers for intercellular communication in health and disease. Nef is a human immunodeficiency virus (HIV) virulence factor that is released from cells within EVs and is present in plasma EVs of HIV-1 infected individuals. We performed a quantitative proteomic analysis to fully characterize the Nef-induced changes in protein composition of T cell-derived EVs and identify novel host targets of HIV. Several proteins with well-described roles in infection or not previously associated with HIV pathogenesis were specifically modulated by Nef in EVs. Among the downregulated proteins are the interferon-induced transmembrane 1, 2 and 3 proteins (IFITM1-3), broad-spectrum antiviral factors known to be cell-to-cell transferable by EVs. Our data establish Nef as a modulator of EVs' global protein content and as an HIV factor that antagonizes IFITMs.

2024-01-26 | PXD041028 | Pride

Gene expression profiling of CD4+ T cell line due to presence of Nef during HIV-1 infection.

Project description:We have utilized microarray technology to compare gene expression profile in presence or absence of Nef during HIV-1 infection in T cell-line. We found several genes significantly differentially regulated due to ∆nef HIV-1 infection and WT HIV-1 infection when compared to Uninfected cells and also several genes significantly dergulated due to WT HIV-1 infection as compared to ∆nef HIV-1 infection. We redistributed genes belonging to several gene ontology into broad categories like “signaling”, “apoptosis”, “transcription” and “lipid metabolism”. We selected some lipid metabolism genes to validate the Nef directed differential expression using quantitative real-time RT-PCR. Thus the present work highlights the importance of Nef directed differential gene expression in milieu of other viral proteins present during infection.

2016-12-06 | GSE76793 | GEO

Probe to gene expressions in HIV infected CD4 T cells in the presence of CDK, caspase inhibitors and Nef

Project description:HIV-1 infection selectively alters gene expressions of CD4 T cells. To understand the effects of HIV to the expressions of CDK and caspase pathway genes in the presence and absence of Nef, we infected CD8-depleted PBMC from healthy donors with HIV-1 BAL in the presence of BB-94, PD-0332991, QVD-OPH or DMSO control, or with Nef-sufficient, Nef-deficient Vpu-sufficient, Vpu-deficient NL4-3 strain of HIV-1. On day 6 of infection, cells were enriched for CD4 T cells for gene expression profile analyses by RNA sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq of 16 different treated CD4 T cells.

2023-11-23 | GSE218175 | GEO

Nef dimerization defect abrogates HIV viremia and associated immune dysregulation in the Bone Marrow-Liver-Thymus-Spleen (BLTS) humanized mouse model.

Project description:Loss of function mutations in the human immunodeficiency virus (HIV)-negative factor (Nef) gene are associated with reduced viremia, robust T cell immune response, and delayed acquired immunodeficiency syndrome (AIDS) progression in humans. Additionally, in vitro studies have shown that mutations in Nef's dimerization interface may play a significant role in modulating viral replication and impairing host defense. However, in vivo, mechanistic studies on the role of Nef dimerization in HIV infection are lacking. Humanized rodent models with human immune cells are robust platforms for investigating the interactions between HIV and the human immune system. We recently developed the bone marrow-liver-thymus-spleen (BLTS) humanized mouse model, which carries human immune cells, as well as primary and secondary lymphoid tissues that facilitate anti-viral immune responses. Here, we employed the BLTS-humanized mouse model to demonstrate that preventing Nef dimerization abrogates HIV viremia and the associated induction of immune dysregulation (immune activation and exhaustion). This suggests that Nef dimerization may be a therapeutic target for future HIV cure strategies, which can be explored in humanized mouse models.

2021-03-10 | GSE165387 | GEO

HIV Nef amplifies mechanical heterogeneity to promote immune evasion

Project description:Intracellular pathogens must evade cytotoxic immunity to establish persistent infection. Although immune escape is typically viewed through a biochemical lens, the ability of certain pathogens to alter mechanical properties of infected cells suggests that biophysical mechanisms may also contribute. Here, we show that a subset of CD4+ T cells infected with the human immunodeficiency virus (HIV) resist elimination through a soft phenotype that impairs killing by mechanosensitive cytotoxic T lymphocytes (CTLs). This phenotype arises from the combined effects of the HIV virulence factor Nef, which remodels the actin cytoskeleton, and intrinsic heterogeneity in basal cytoskeletal properties of T cells. Although cells that are sufficiently soft to resist CTLs are relatively rare, this property can be detected in HIV-infected CD4+ T cell clones from people living with HIV, implicating a role for this mechanism in reservoir persistence. These findings define a biophysical paradigm of immune evasion with implications for HIV cure strategies.

2025-11-29 | GSE311304 | GEO

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