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One way or another: Differential impact of pharmacologic inhibitors on extracellular vesicles derived from resting neutrophils

ABSTRACT: We performed a systematic investigation of seven pharmacologic inhibitors (calpeptin, D-pantethine, Y27632, cytochalasin D, GW4869, R5421, and Nexinhib20) on quantitative and qualitative EV properties derived from resting neutrophils. We measured EV numbers, size distribution, total lipid, protein, and RNA content. We also analyzed the EV morphology by cryo-EM and EV cargo qualitatively by mass spectrometry and RNA sequencing (mRNA, miRNA).

INSTRUMENT(S): Illumina NovaSeq X

ORGANISM(S): Homo sapiens

SUBMITTER: Viktoria Szeifert

PROVIDER: E-MTAB-15976 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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One way or another: Differential impact of pharmacologic inhibitors on extracellular vesicles derived from resting neutrophils

Project description:We performed a systematic investigation of seven pharmacologic inhibitors (calpeptin, D-pantethine, Y27632, cytochalasin D, GW4869, R5421, and Nexinhib20) on quantitative and qualitative EV properties derived from resting neutrophils. We measured EV numbers, size distribution, total lipid, protein, and RNA content. We also analyzed the EV morphology by cryo-EM and EV cargo qualitatively by mass spectrometry and RNA sequencing (mRNA, miRNA).

2025-11-24 | E-MTAB-15978 | biostudies-arrayexpress

miRNA profiling of extracellular vesicled derived from acute lymphoblastic leukemic cell line 697 treated with ActivinA against untreated cells

Project description:Role of ActivinA in the modulation of EV-miRNA cargo in acute lymphoblastic leukemic cell line 697.

2024-06-18 | E-MTAB-14003 | biostudies-arrayexpress

Extracellular Vesicles from patients with Antibody-Mediated Rejection induce tubular senescence and endothelial to mesenchymal transition by regulating complement activation through horizontal transfer of miRNAs

Project description:Extracellular vesicles (EV) has been shown to deliver potential microRNA (miRNA) as cargo for specific target cells; effectively, the EV unique nature of the bilayer allows miRNA to be protected from degradation. We used microarray analysis to compare the miRNA profiles of EV isolated from acute antibody-mediated allograft rejection patients (AAMR) and chronic antibody-mediated allograft rejection (CAMR) compared to Tx Controls patients. By microarray miRNA profiling we detected 42 miRNAs downregulated and 34 miRNAs upregulated with FDR < 0.05 and Fold change >2. Principal Component analysis showed that these 76 miRNAs were able to distinguish AMR-derived EV from healthy TX patients. We also investigated whether differences in EV miRNA content could separate AAMR and CAMR patients. We found 9 miRNAs differentially expressed in the two AMR groups (eight downregulated and only one upregulated in AAMR compared to CAMR; effectively, these miRNAs could distinguish AAMR-derived EV from CAMR-derived EV. We then investigated the possible target genes of these miRNAs according to their expression, fold change and the p value; interestingly, several targets were associated to CDKN1A and CDKN2A genes regulation.

2021-09-10 | E-MTAB-10447 | biostudies-arrayexpress

Genome-wide analysis of gene expression of IWR1/Y27632-maintained epiblast stem cells (EpiSCs)

Project description:Analysis of specific genes regulated by IWR1 and Y27632 (Y27), respectivly. Total RNA obtained from No Treatment (NT) control EpiSCs and EpiSCs treated by 2 ÂµM IWR1 or 0.5 ÂµM Y27.

2016-06-01 | E-GEOD-77476 | biostudies-arrayexpress

Matrix stiffness modulated release of spheroid-derived extracellular vesicles and discovery of Piezo1 cargo [miRNA-seq]

Project description:Augmented extracellular matrix (ECM) stiffness is a mechanical hallmark of cancer. Mechanotransduction studies have extensively probed the mechanisms by which ECM stiffness regulates intracellular communication. However, the influence of stiffness on intercellular communication aiding tumor progression in three-dimensional microenvironments remains unknown. Small extracellular vesicles (EVs) are communicators of altered biophysical cues to distant sites through EV-ECM interactions and EV-mediated recipient cell-ECM interactions. Here we demonstrate stiffness-mediated modulation of small EVs secretion and cargo from three-dimensional oral squamous cell carcinoma spheroids. Using a spheroid culture platform with varying matrix stiffness properties, we show that small EVs carry parental biomolecular cargo, including mechanosensitive Piezo1 ion channel and adhesion molecule CD44. We comprehensively validate the presence of both markers in our EV populations using proteomic and genetic analysis. Transcriptomic analysis of microRNA and long non-coding RNA cargo of small EVs released from soft and stiff ECM spheroids revealed enrichment of tumorigenic and metastatic profiles in EVs from stiff ECM cultures compared to that of soft ones. Gene set enrichment analysis of a comparative dataset obtained by overlaying spheroid mRNA and EV miRNA profiles identified key oncogenic pathways involved in cell-EV crosstalk in the spheroid model.

2026-01-27 | GSE288252 | GEO

Matrix stiffness modulated release of spheroid-derived extracellular vesicles and discovery of Piezo1 cargo [mRNA]

2026-01-27 | GSE288247 | GEO

Obese adipose tissue extracellular vesicles activate mitochondrial fatty acid -oxidation to drive colonic stemness

Project description:Obesity increases the risk of colorectal cancer (CRC) development and accelerates disease progression. Obesity adversely affects the visceral adipose tissue (VAT) leading to increased secretion of extracellular vesicles (EVs). However, the crosstalk between VAT and CRC tumor cells still remains unclear. EVs are lipid-membraned particles that transfer cargo to and/or induce signaling in other cells. Here, human VAT-derived non-obese (N-OB) and obese (OB) EVs through proteomics and investigated the functional interaction between CRC cells and EVs through RNA-seq analysis of EV-treated CRC cells. EVs were isolated from VAT obtained from obese (BMI>30) and non-obese patients (BMI<30). Unbiased proteomics revealed that compared to N-OB EVs, OB EVs were enriched with glycolytic enzymes like triose phosphate isomerase (TPI1). This enrichment was associated with increased TPI1 protein levels in CRC cells and elevated glycolytic activity. OB EV-treated cells also exhibited increased stemness-associated genes, 3D-spheroid formation and Apcmin/+ tumoroid self-renewal capacity. In vivo, mice with an adipocyte-specific knockout of EV cargo sorting protein, Tsg101 (Tsg101ΔAd), have altered EV cargo composition with reduced glycolytic enzyme levels. Functionally, Tsg101ΔAd-EVs were able to protect against high-fat diet (HFD)-induced increase in glycolysis and stem-like ability. Moreover, Apcmin/+:Tsg101ΔAd mice were protected against HFD-induced enhanced tumorigenesis. Collectively, this study identifies adipocyte EVs, and its metabolic cargo, as an important regulator of CRC cell metabolism and function, promoting intestinal tumorigenesis.

2025-12-10 | GSE291093 | GEO

Fibroblast-derived extracellular vesicles contain SFRP1 and mediate pulmonary fibrosis

Project description:Idiopathic pulmonary fibrosis (IPF) is a lethal chronic lung disease characterized by aberrant intercellular communication, extracellular matrix deposition and destruction of functional lung tissue. While extracellular vesicles (EVs) accumulate in the IPF lung, their cargo and biological effects remain unclear. We interrogated the proteome of EV and non-EV fractions during pulmonary fibrosis and characterize their contribution to fibrosis. EVs accumulated 14 days post-bleomycin challenge, correlating with decreased lung function and initiated fibrogenesis in healthy precision-cut lung slices. Label-free proteomics of broncho-alveolar lavage fluid (BALF)-EVs collected from mice challenged with bleomycin or control identified 107 proteins enriched in fibrotic vesicles. Multiomic analysis revealed fibroblasts as a major cellular source of BALF-EV cargo, which was enriched in Secreted Frizzled Related Protein 1 (SFRP1). Sfrp1 deficiency inhibited the activity of fibroblast-derived EVs to potentiate lung fibrosis in vivo. SFRP1 led to increased transitional cell markers, such as Krt8, and WNT/β-catenin signaling in primary alveolar type 2 cells. SFRP1 is expressed within the IPF lung and localized at the surface of EVs from patient-derived fibroblasts and BALF. Our work reveals altered EV protein cargo in fibrotic EVs promoting fibrogenesis and identifies fibroblast derived vesicular SFRP1 as fibrotic mediator and potential therapeutic target for IPF.

2024-11-05 | GSE272679 | GEO

Aspirin Repurposing in Folate-Decorated Nanoparticles: Another Way to Target Breast Cancer.

Project description: Not available

| S-EPMC8848101 | biostudies-literature

Comparison of extracellular vesicles isolation methods reveals method-dependent protein and miRNA profiles in saliva

Project description:Salivary extracellular vesicles (EVs) represent a powerful, non-invasive source of biomarkers for disease diagnosis and monitoring. Their molecular cargo reflects systemic and local physiological states, offering a window into neurological and inflammatory disorders. However, the diversity of EV isolation protocols and the possibility that each enriches distinct EV subpopulations remains a major barrier to reproducibility and data comparability. We conducted a comprehensive comparison of three EV isolation methods: ultracentrifugation (UC), PEG-based precipitation (Q), and immunoaffinity capture (M) to evaluate their impact on EV yield, purity, and molecular composition. Salivary EVs from healthy volunteers were analysed using proteomic and small-RNA sequencing approaches. Principal component analysis revealed clear isolation method-dependent clustering, where M-derived EVs displayed the most distinct profile. UC and Q produced broader proteomic repertoires with higher total protein content, whereas M-isolated EVs exhibited greater purity and enrichment of trafficking- and lysosome-associated proteins. Over 731 miRNAs selected, 28 were consistently altered across methods and 65 uniquely enriched in M isolates. RT-qPCR confirmed key directional trends. These 93 method-dependent miRNAs have predicted targets associated with synaptic structure and neurodegenerative pathways. These findings show that isolation methodology deeply shapes salivary EV cargo and suggest that immunoaffinity capture can isolate specific EV populations meeting diagnostic requirements.

2025-12-05 | GSE312585 | GEO

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