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Extracellular vesicle subtypes from human colorectal cancer cell lines

ABSTRACT: This study focuses on characterisation of three extracellular vesicle subtypes (sEVs/Exos, lEVs/MPs and sMB-Rs) using proteomic approach.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Colon

DISEASE(S): Colon Cancer

SUBMITTER: Wittaya Suwakulsiri

LAB HEAD: Rciahrd Johm Simpson

PROVIDER: PXD041529 | Pride | 2025-06-27

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	480_Exos_1A.raw	Raw
	480_Exos_1B.raw	Raw
	480_Exos_2A.raw	Raw
	480_Exos_2B.raw	Raw
	480_Exos_3A.raw	Raw

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1 - 5 of 37

Publications

Comparative proteomic analysis of three major extracellular vesicle classes secreted from human primary and metastatic colorectal cancer cells: Exosomes, microparticles, and shed midbody remnants.

Suwakulsiri Wittaya W Xu Rong R Rai Alin A Shafiq Adnan A Chen Maoshan M Greening David W DW Simpson Richard J RJ

Proteomics 20230728 11

Cell-derived extracellular vesicles (EVs) are evolutionary-conserved secretory organelles that, based on their molecular composition, are important intercellular signaling regulators. At least three classes of circulating EVs are known based on mechanism of biogenesis: exosomes (sEVs/Exos), microparticles (lEVs/MPs), and shed midbody remnants (lEVs/sMB-Rs). sEVs/Exos are of endosomal pathway origin, microparticles (lEVs/MPs) from plasma membrane blebbing and shed midbody remnants (lEVs/sMB-Rs) a ...[more]

PMID: 37507836

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Proteome analysis of epithelial-mesenchymal transition extracellular vesicles: exosomes, microparticles and shed midbody remnants

Project description:Cell-derived extracellular vesicles (EVs) are evolutionary-conserved secretory organelles that, based on their molecular composition, are important intercellular signaling regulators. At least three classes of circulating EVs are known based on mechanism of biogenesis: exosomes (sEVs/Exos), microparticles (lEVs/MPs) and shed midbody remnants (lEVs/sMB-Rs). Here we conducted large-scale purification of exosomes, MPs and sMBRs isolated from MDCK and 21D1 cells, and performed comprehensive proteomics analysis to differentiate these EV subtypes. Findings from this study suggests that sMBRs may hold crucial clues to the regulation of EMT and the involvement of different subtypes of EVs based on their dynamic proteome landscape in this process.

2023-10-04 | MSV000093044 | MassIVE

Different RNA profiles in plasma derived small and large extracellular vesicles of Neurodegenerative diseases patients.

Project description:We detected different deregulated RNAs in LEVs and SEVs from patients with Alzheimer's, Parkinson's Disease, Amyotrophic Lateral Sclerosis, ALS. MiRNAs resulted to be the most interesting subpopulation of transcripts transported by plasma derived SEVs since they appeared to discriminate all NDs disease from CTRLs and they can provide a signature for each NDs. Common enriched pathways for SEVs were mainly linked to ubiquitin mediated proteolysis and Toll-like receptor signaling pathways and for LEVs to neurotrophin signaling and Glycosphingolipid biosynthesis pathway.

2020-08-05 | GSE155700 | GEO

Characterization of extracellular vesicle miRNA cargos from mouse bone

Project description:EVs are known to play an important role in communication between bone cells. However, few studies have been carried out on EVs derived from osteocytes. The main aim of this project was to collect, characterize and evaluate the potential osteogenic properties of EVs derived from bone, composed of 95% osteocytes. Two subpopulations of EVs, large EVs (lEVs) and small EVs (sEVs), were isolated by differential centrifugation from Swiss male mouse long bone cortices and were characterized from a physico-chemical and functional point of view. Identification of protein and miRNA cargos associated with lEVs and sEVs was carried out by proteomics and small RNA-Seq respectively.

2025-09-30 | GSE250170 | GEO

Transcriptomic analysis and fusion gene identification of Exos, MPs, MBRs

Project description:Previously, we reported that human primary (SW480) and metastatic (SW620) colorectal (CRC) cells secrete (shed) midbody remnants (MBRs), exosomes (Exos), and microparticles (MPs) are molecularly distinct at the protein level. To gain further biochemical insights into MBRs, Exos, and MPs and their emerging role in CRC, we performed, and report here for the first time, a comprehensive transcriptome and long noncoding RNA sequencing analysis and fusion gene identification of these three EV classes using the next-generation RNA sequencing technique. Differential transcript expression analysis revealed that MBRs have a distinct transcriptomic profile compared to Exos and MPs with a high enrichment of mitochondrial transcripts lncRNA/pseudogene transcripts that are predicted to bind to ribonucleoprotein complexes, spliceosome and RNA/stress granule proteins. A salient finding from this study is a high enrichment of several fusion genes in MBRs compared to Exos, MPs and cell lysates from their parental cells such as MSH2 (gene encoded DNA mismatch repair protein MSH2). This suggests potential EV-liquid biopsy targets for cancer detection. Importantly, the expression of cancer progression-related transcripts found in EV classes derived from SW480 (EGFR) and SW620 (MET and MACCA1) cell lines reflects their parental cell types. Our study is the first discovery of RNA and fusion gene compositions within MBRs (including Exos and MPs) that could have an impact on EV functionality in cancer progression and detection using EV-based RNA/ fusion gene candidates for cancer biomarkers

2024-02-26 | GSE244455 | GEO

Unbiased miRNA screening analysis on myo-sEVs derived from Nor or HG/HL

Project description:The current study aims were to determine the differential expression of Myo-sEVs derived from normal or HG/HL.Mouse primary myocardial cells were isolated and cultured in normal and HG/HL culture medium. Myo-sEVs were separated by ultracentrifugation.Differential myo-sEVs-miRNA expression obtained through Unbiased miRNA array analysis.

2024-02-07 | E-MTAB-13736 | biostudies-arrayexpress

Small Extracellular Vesicles from Radioresistant H3K27M-Pediatric Diffuse Midline Glioma Cells Modulate Tumor Phenotypes and Radiation Response [smRNA-Seq]

Project description:Pediatric diffuse midline gliomas harboring the Histone 3 lysine 27-to-methionine mutation (H3K27M-pDMG) represent a highly heterogenous group of brain tumors characterized by intrinsic resistance to radiation therapy, the current standard of care. Recent evidence suggests that intratumor small extracellular vesicle (sEV)-mediated signaling plays an oncogenic role among glioma stem cell populations. However, the dynamics and functional roles of H3K27M-pDMG derived sEVs in the context of radiation-induced stress remain unclear. In this study, we characterize sEV uptake dynamics between H3K27M tumor cells, identify potential sEV surface proteins involved in the process, and demonstrate that radioresistant (RR) H3K27M-pDMG-derived sEVs confer radioprotective effects to radiosensitive (RS) H3K27M-pDMG cells at the population level. RR-sEVs induce metabolic and gene expression changes in RS cell populations within the timescale of EV uptake and internalization, leading to improved DNA repair following radiation-induced stress. Furthermore, we identified the proteins, microRNAs (miRNAs), and metabolites present in RR-sEVs, shedding light on the molecular cargo that may be responsible for these effects. Our findings provide insights into the intrinsic radioresistant properties mediated by H3K27M-pDMG-derived sEVs and propose novel targets for disrupting radioresistant intratumoral communication in H3K27M-pDMGs.

2025-06-02 | GSE286943 | GEO

Small Extracellular Vesicles from Radioresistant H3K27M-Pediatric Diffuse Midline Glioma Cells Modulate Tumor Phenotypes and Radiation Response [EVtreat_RNA-Seq]

2025-06-02 | GSE286941 | GEO

Small Extracellular Vesicles from Radioresistant H3K27M-Pediatric Diffuse Midline Glioma Cells Modulate Tumor Phenotypes and Radiation Response [bulk RNA-seq]

2025-06-02 | GSE286945 | GEO

Transcriptomic analysis and fusion gene identification of Exos, MPs, MBRs

Project description:Transcriptomic analysis and fusion gene identification of Exos, MPs, MBRs

| PRJNA1023206 | ENA

RNA-Seq for primary rat Kupffer cells and monocytes treated with hepatic stellate cell-derived small extracellular vesicles

Project description:Aim: To find out the effects of small extracellular vesicles (sEVs) from short-term activated and long-term activated hepatic stellate cells (HSCs) on Kupffer cells (KCs) and bone marrow-derived monocytes (MOs). Methods: For the isolation of HSC-derived sEVs, culture media (CMs) from Day 0 to Day 3 and Day 7 to Day 14 were collected. The sEVs from Day 0 to Day 3 HSC CMs were referred to as short-term activated HSC-sEVs (3dHSC-sEVs), and those from Day 7 to Day 14 HSC CMs were referred to as long-term activated HSC-sEVs (14dHSC-sEVs). Purified primary rat KCs and MOs were cocultured with 3dHSC- or 14dHSC-sEVs for 48 h. HSC-sEVs cocultured KCs or MOs were lysed in TRIzol (Life Technologies) for RNA sample preparation at the indicated time points.

2024-08-29 | E-MTAB-12754 | biostudies-arrayexpress

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