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ScRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Patient]

ABSTRACT: scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Patient]

PROVIDER: PRJNA830878 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18890375.fastq.gz	Fastqsanger.gz
	SRR18890376.fastq.gz	Fastqsanger.gz
	SRR18890377.fastq.gz	Fastqsanger.gz
	SRR18890378.fastq.gz	Fastqsanger.gz

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scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Exp2]

Project description:scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Exp2]

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scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Patient]

Project description:Primary DC from HIV-1-infected patient during primo-infection were isolated to study their transcriptom by scRNA-seq

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scRNA-Seq to study the impact of HIV-1 on pre-DC biology [PreDC_Single_Cell_Exp1]

Project description:scRNA-Seq to study the impact of HIV-1 on pre-DC biology [PreDC_Single_Cell_Exp1]

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scRNA-Seq to study the impact of HIV-1 on DC biology [PreDC_Single_Cell_Exp2]

Project description:Pre-DC have been initially described through their ontogeny. Our lab reported for the first time a pre-DC functional specificity in the context of HV-1 capture, infection and in vitro transmission as a consequence of their constitutive expression of Siglec-1. However, pre-DC immune response to viral exposure remained to be studied. This study aim to decipher innate immune response of pre-DC and cDC2 when exposed to HIV-1 in the presence or not of Vpx.

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scRNA-Seq to study the impact of HIV-1 on pre-DC biology [PreDC_Single_Cell_Exp1]

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DC-SIGN initiates an immature dendritic cell phenotype triggering Rho activation that is utilised by HIV-1

Project description:DC-SIGN is a C-type lectin expressed by dendritic cells (DCs) that binds HIV-1, sequestering it within multivesicular bodies to facilitate transmission to CD4+ T cells. Here we characterize the molecular basis of signalling through DC-SIGN by large-scale gene expression profiling and phosphoproteome analysis. Solitary DC-SIGN activation leads to a phenotypically disparate transcriptional program from Toll-like receptor (TLR) triggering with downregulation of MHC II, CD86, and interferon response genes and with induction of the TLR negative regulator ATF3. Phosphoproteome analysis reveals DC-SIGN signals through the leukemia-associated Rho guanine nucleotide exchange factor (LARG) to induce Rho activity. This LARG activation also occurs on DC HIV exposure and is required for effective HIV viral synapse formation. Taken together HIV mediated DC-SIGN signalling provides a mechanism by which HIV evades the immune response yet induces viral spread. Keywords: Activation state, signalling, Toll-like Receptor (TLR)

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DC immunotherapy in HIV-1 infection induces a major blood transcriptome shift

Project description:Objective: This study aimed to evaluate the effect of dendritic cell (DC) vaccination against HIV-1 on host gene expression profiles. Design: Longitudinal PBMC samples were collected from participants of the DC-TRN trial for immunotherapy against HIV. Microarray-assisted gene expression profiling was performed to evaluate the effects of vaccination and subsequent interruption of antiretroviral therapy on host genome expression. Data from the DC-TRN trial were compared with results from other vaccination trials. Methods: We used Affymetrix GeneChips for microarray gene expression analysis. Data were analyzed by principal component analysis and differential gene expression was assessed using linear modeling. Gene ontology enrichment and gene set analysis were used to characterize differentially expressed genes. Transcriptome analysis included comparison with PBMCs obtained from DC-vaccinated melanoma patients and of healthy individuals who received seasonal influenza vaccination. Results: DC-TRN immunotherapy in HIV-infected individuals resulted in a major shift in the transcriptome. Longitudinal analysis demonstrated that changes in the transcriptome sustained also during interruption of antiretroviral therapy. After DC-vaccination, the transcriptome was enriched for cellular immunity associated genes that were also induced in healthy adults who received live attenuated influenza virus vaccination. These beneficial responses were accompanied by detrimental signals of general immune activation. Conclusions: The DC-TRN induced changes in the transcriptome were profound, lasting, and consisted of both protective signals and signatures of inflammation and immune exhaustion, with a net result of decreased viral load, without clinical benefit. Thus transcriptome analysis provides useful information, dissecting both positive and negative effects, for the evaluation of safety and efficacy of immunotherapeutic strategies.

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Transcription profiling of human monocyte derived dendritic cells treated with DC-SIGN initiates an immature dendritic cell phenotype triggering Rho activation that is utilised by HIV-1

Project description:DC-SIGN is a C-type lectin expressed by dendritic cells (DCs) that binds HIV-1, sequestering it within multivesicular bodies to facilitate transmission to CD4+ T cells. Here we characterize the molecular basis of signalling through DC-SIGN by large-scale gene expression profiling and phosphoproteome analysis. Solitary DC-SIGN activation leads to a phenotypically disparate transcriptional program from Toll-like receptor (TLR) triggering with downregulation of MHC II, CD86, and interferon response genes and with induction of the TLR negative regulator ATF3. Phosphoproteome analysis reveals DC-SIGN signals through the leukemia-associated Rho guanine nucleotide exchange factor (LARG) to induce Rho activity. This LARG activation also occurs on DC HIV exposure and is required for effective HIV viral synapse formation. Taken together HIV mediated DC-SIGN signalling provides a mechanism by which HIV evades the immune response yet induces viral spread. Experiment Overall Design: Circulating monocyte derived DCs were isolated from buffy coats by adherence and culture in IL-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF). DC preparations analyzed were more than 98% pure. At day four 10 million immature DCs were either left unstimulated or stimulated using plate bound anti-DC-SIGN antibody for 2 hr. Three replicates of non-stimulated or stimulated cells were taken and used to extract total RNA.

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