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Analysis of small EV proteomes reveals unique functional protein networks regulated by VAP-A

ABSTRACT: VAP-A regulates extracellular vesicle biogenesis at ER-membrane contact sites. Proteomic analysis of purified small extracellular vesicles from control (Sc) and VAP-A-KD (KD1 and KD2) DKs-8 cells were conducted.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Marisol Ramirez

LAB HEAD: Alissa Weaver

PROVIDER: PXD043796 | Pride | 2023-11-10

REPOSITORIES: Pride

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VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites

Project description:RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCS) as platforms for generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes lumenal filling of multivesicular bodies (MVBs). CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives biogenesis of a select RNA-containing population.

2022-04-05 | GSE188223 | GEO

Uropathogenic Escherichia coli biofilm proteomics

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Comparison of gene expression in melanoma of wild-type and VAP-1 -/- mice

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Developing a gene expression model for predicting ventilator-associated pneumonia in trauma patients: a pilot study.

Project description:Objective: Identify genes that are differentially expressed between critically ill trauma patients who go on to develop ventilator-associated pneumonia (VAP) compared to similar patients who do not develop VAP Using gene expression differences, develop a model that predicts which patients are at greater risk of developing VAP.

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Exosomes secreted by a nematode parasite transfer small RNAs to mammalian cells and regulate genes of the innate immune system [Heligmosomoides polygyrus]

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2014-11-25 | E-GEOD-55978 | biostudies-arrayexpress

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Project description:Extracellular vesicles (Evs) from proliferating myogenic progenitor cells (MPCs) were isolated and RNA was profiled via miRNA microarray

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Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (scRNA-seq)

Project description:We preformed a systems biological assessment of lower respiratory tract host immune responses and microbiome dynamics in COVD-19 patients, using bulk RNA-sequencing, single-cell RNA sequencing, and techniques, and microbiome analysis. Are focus was on differential gene expression in severe COVID-19 patients who developed ventilator associated pneumonia (VAP) during their course versus severe COVID-19 patients who did not develop VAP. We found early impairment in antibacterial immune signaling in patients two or more weeks prior to the development of VAP, compared to COVID-19 patients who did not develop VAP. There was no signficant difference in viral load, but an association of disruption in lung microbiome by alpha and beta diversity metrics was also found.

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Impaired antibacterial immune signaling and changes in the lung microbiome precedes secondary bacterial pneumonia in COVID-19 (bulkRNA-seq)

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Comparison of gene expression in melanoma of wild-type and VAP-1 -/- mice

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2010-04-07 | E-GEOD-13626 | biostudies-arrayexpress

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