Dataset Information

Altered Extracellular Vesicle-derived protein and microRNA signatures in bronchoalveolar lavage fluid from COPD patients

ABSTRACT: Abstract: Chronic obstructive pulmonary disease (COPD) is a progressive lung disease for which there is no cure. Accumulating research results suggest a role for extracellular vesicles (EVs) in the pathogenesis of COPD. This study aimed to uncover the involvement of EVs and their molecular cargo in the progression of COPD by identification of EV-associated protein and microRNA (miRNA) profiles. We isolated EVs from bronchial alveolar lavage fluid (BALF) of 18 patients with COPD and 11 healthy controls by size exclusion chromatography. EV isolates were characterized by Nnanoparticle tracking analysis and protein content. Proteomic analysis revealed higher abundance of 284 proteins (log2FC > 1) and lower abun-dance of 3 proteins (log2FC <-1) in EVs derived from patients with COPD. Ingenuity pathway analysis showed that proteins enriched in COPD-associated EVs trigger inflammatory responses including neutrophil degranulation. Variances in surface receptors and ligands associated with COPD EVs suggested preferential interaction with alveolar cells. Small RNAseq analysis iden-tified higher abundance of ten miRNAs and lower abundance of one in EVs from COPD versus controls (Basemean >100, FDR<0.05). Our data indicate that the molecular composition of EVs in BALF of patients with COPD is altered compared to healthy control EVs. Several components in COPD EVs were identified that may perpetuate inflammation and alveolar tissue destruction.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Extracellular Vesicle, Bronchoalveolar Lavage

DISEASE(S): Chronic Obstructive Pulmonary Disease

SUBMITTER: Justina Clarinda Wolters

LAB HEAD: Justina Clarinda Wolters

PROVIDER: PXD049998 | Pride | 2024-06-23

REPOSITORIES: Pride

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			Action	DRS
	2021-25_70percentfilteredoutput.xlsx	Xlsx
	210611_2021-25_S1.raw	Raw
	210611_2021-25_S10.raw	Raw
	210611_2021-25_S11.raw	Raw
	210611_2021-25_S12.raw	Raw

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Publications

Altered Extracellular Vesicle-Derived Protein and microRNA Signatures in Bronchoalveolar Lavage Fluid from Patients with Chronic Obstructive Pulmonary Disease.

Bartel Sabine S Wolters Justina C JC Noor Hasnat H Rafie Karim K Fang Jiahua J Kirchner Benedikt B Nolte-T Hoen Esther E Pfaffl Michael W MW Rutgers Steven S Timens Wim W van den Berge Maarten M Hylkema Machteld N MN

Cells 20240530 11

Chronic obstructive pulmonary disease (COPD) is a progressive lung disease for which there is no cure. Accumulating research results suggest a role for extracellular vesicles (EVs) in the pathogenesis of COPD. This study aimed to uncover the involvement of EVs and their molecular cargo in the progression of COPD by identification of EV-associated protein and microRNA (miRNA) profiles. We isolated EVs from the bronchial alveolar lavage fluid (BALF) of 18 patients with COPD and 11 healthy controls ...[more]

PMID: 38891077

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Project description:Background: Acute coronary syndromes (ACS) are associated with aberrant gene expression and epigenetic mechanisms. In particular, de novo DNA methylation is typically linked to gene silencing, but its role in heart disease remains not fully understood. Extracellular vesicles (EVs) are active components in cellular communication for their ability to carry a plethora of signalling biomolecules, thus representing a promising new diagnostic/therapeutic approach in cardiovascular diseases (CVDs). Indeed, there is the need of novel biomarkers for ACS prediction and timely detection. Purpose: We hypothesized that specific epigenetic signals can be carried by EVs. In this regard, we isolated and characterized circulating EVs from ACS patients and evaluated their potential role to influence DNA methylation in target cells. Methods: Circulating EVs were recovered, by ultracentrifugation, from plasma samples of 19 ACS patients and 50 healthy subjects (HS). Nanoparticle tracking analysis (NTA) and western blot (WB) were used to confirm the EVs integrity and purity. Peripheral blood mononuclear cells (PBMCs) of volunteer donors were treated with both ACS and HS derived EVs and genomic DNA was extracted to perform epigenome wide analysis through Reduced Representation Bisulfite Sequencing. ShinyGO, PANTHER, and STRING tools were interrogated to perform GO and PPI network analyses. Flow Cytometry, qRT-PCR, and WB analysis were also performed to evaluate and validate both intra-vesicular and intra-cellular signals. Results: Plasma ACS-derived EVs showed a significant up-regulation of DNA methyltransferases (DNMTs) gene expression levels as compared to HS (P<0.001). Specifically, de novo methylation transcripts, as DNMT3A and DNMT3B were significantly increased in plasma ACS-EVs. DNA methylation analysis of PBMCs from volunteer donors treated with HS- and ACS-derived EVs showed that RNF166 and CCND3 genes resulted the most hyper- and hypo-methylated, respectively, after by ACS-EV treatment. In addition, PPI network analysis specifically evidenced the subnetwork with SRC, as a hub gene, connecting it to NOTCH1, FOXO3, CDC42, IKBKG, RXRA, DGKG, known as important genes already involved in the onset of CVDs. Surprising, other novel genes, BAIAP2, SYP, CHL1, and SHB, which were hypomethylated, were found significantly overexpressed in PBMCs (P<0.005), underlying the fundamental modulating properties of EV cargo in atherosclerosis. Conclusions: These findings support the significant role of ACS plasma-derived EVs, inducing de novo DNA methylation signals, and modulating specific signaling pathways in target cells.