Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive analysis of supermere, exomere, and extracellular vesicle isolation and cargo in colorectal cancer

ABSTRACT: Biofluids contain a heterogeneous mixture of extracellular vesicles and non-vesicular nanoparticles (including exomeres and supermeres) that transport a diverse array of proteins, RNA, and lipids. Our previous efforts to characterize the contents of these carriers in colorectal cancer relied on 2D culture systems requiring large-scale setups and time-consuming ultracentrifugation-based isolation. To streamline this process, we have combined 3D hollow-fiber bioreactor production and fast-protein liquid chromatography-based size-exclusion chromatography. Here, we compare the impact of culture methods and purification strategies on small extracellular vesicle, exomere and supermere cargo. Proteomic analyses show distinct profiles for extracellular vesicles, exomeres, and supermeres consistent regardless of culture conditions or isolation method. In contrast, these two variables influence small RNAs, their base modifications, and lipidomic profiles. We present an online tool to query these and future secretome datasets (https:/superomics.shinyapps.io/browse).

ORGANISM(S): Homo sapiens

PROVIDER: GSE304273 | GEO | 2025/12/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Proteome of DiFi EVs, exomeres and supermeres purified by ultracentrifugation and FPLC

Project description:The cell seretome is diverse and contains extracellular secreted vesicles (EVs) as well as non-vesicular extracellular nanoparticles (NVEPs) called exomeres and supermeres, all of which carry different kinds of cell signaling cargos. We have developed new techniques to purify exomeres and supermeres by ultracentrifugation (UC) and by fast protein liquid chromatography (FPLC) from cell conditioned media and from blood plasma. We utilized a proteomics approach to compare UC and FPLC methods with standard UC and density gradient methods of isolating EVs and new methods of isolating NVEPs. We acquired LC-MS/MS data from conditioned media using standard 2D plastic and hollow fiber 3D bioreactor production from a CRC cell line, DiFi, using all these methods and growth culture conditions.

2025-09-11 | PXD066872 | Pride

Proteome of DiFi and CC-CR supermeres purified by FPLC with or without additional affinity purification for TGFBi

Project description:The cell seretome is diverse and contains extracellular secreted vesicles (EVs) as well as non-vesicular extracellular nanoparticles (NVEPs) called exomeres and supermeres, all of which carry different kinds of cell signaling cargos. One supermere enriched cargo is transforming growth factor beta induced (TGFBi) protein. We have created TGFBi-neon green-His tagged expressing cell lines in the microsatellite stable (MSS) colorectal cancer cell line DiFi and another one in CC-CR cells with microsatellite instability (MSI). We have developed a fast protein liquid chromatography (FPLC) method for isolating EVs, exomeres and supermeres from biofluids. We used either FPLC or FPLC and then nickel columns that bind His tags to isolate supermeres from DiFi or CC-CR cells. We utilized a proteomics approach acquiring LC-MS/MS data to compare FPLC to FPLC and His tagged TGFBi-containing purified supermeres from DiFi and CC-CR cells. This was done using hollow fiber 3D bioreactor production of conditioned media from these cell lines.

2025-09-11 | PXD066888 | Pride

Diversity and Heterogeneity of Extracellular Vesicles and Brain-Penetrating Amembranous Non-Vesicular Nanoparticles in Glioblastoma

Project description:Advances in understanding intercellular communication through extracellular vesicles (EVs) and non-vesicular extracellular nanoparticles (NVEPs) have been limited by their cellular heterogeneity and unclear origins. Using sequential ultracentrifugation, we identified high- and low-density EVs and performed multi-omics analyses on four EV/NVEP categories, including supermeres. Our findings reveal that extracellular RNA, RNA-binding proteins, and other cellular proteins are differentially expressed among EVs and NVEPs. Notably, supermeres can penetrate the blood-brain barrier, in a manner dependent on their intact RNA and protein structure, and distribute throughout the CNS. Supermeres preferentially interact with microglia at higher levels than other CNS cell types. These interactions lead to decreased TGFβ expression, suggesting an immunomodulatory role. This study highlights supermeres as a promising platform for CNS therapeutic delivery.

2025-11-18 | GSE286513 | GEO

Carrier Subclass Year 4

Project description:To evaluate performance of immunomagnetic separation and size exclusion chromatography in the isolation of different extracellular RNA carriers from biofluids.

2024-12-16 | GSE281131 | GEO

Carrier Subclass

Project description:To evaluate performance of immunomagnetic separation, differential ultracentrifugation and size exculsion chromatography in the isolation of different extracellular RNA carriers from biofluids.

2024-10-31 | GSE246010 | GEO

Diversity and Heterogeneity of Extracellular Vesicles and Brain-Penetrating Amembranous Non-Vesicular Nanoparticles in Glioblastoma

2025-10-13 | PXD059671 | Pride

Supermeres in breast and pancreatic cancer cells

Project description:Extracellular vesicles, including exosomes, and exomere nanoparticles, are under intense investigation for cargo that may serve as clinical biomarkers or therapeutic targets. Here, we report discovery of a new extracellular nanoparticle, termed supermeres. We performed LC/MS-MS proteomics analyses on gradient-purified sEVs, NVs, exomeres and supermeres. The proteomic profile of supermeres is clearly distinct from that of sEVs, NVs and exomeres. This study identifies a new functional nanoparticle replete with potential circulating biomarkers and therapeutic targets that can be exploited for clinical benefit in a host of diseases.

2021-12-01 | PXD027258 | Pride

Supermeres, a new functional extracellular nanoparticle replete with disease biomarkers and therapeutic target

Project description:Extracellular vesicles, including exosomes, and exomere nanoparticles, are under intense investigation for cargo that may serve as clinical biomarkers or therapeutic targets. Here, we report discovery of a new extracellular nanoparticle, termed supermeres. We performed LC/MS-MS proteomics analyses on gradient-purified sEVs, NVs, exomeres and supermeres. The proteomic profile of supermeres is clearly distinct from that of sEVs, NVs and exomeres This study identifies a new functional nanoparticle replete with potential circulating biomarkers and therapeutic targets that can be exploited for clinical benefit in a host of diseases.

2021-11-02 | PXD025213 | Pride

Characterization of tumor extracellular vesicle RNA cargo

Project description:Comparative RNA profiling between tumor cells and their secreted extracellular vesicles. Results revealed enrichment in genes involved in cellular migration and metastasis in extracellular vesicles, in agreement with their role as mediators of tumor progression. Mice were orthotoplically transplanted with MDA-MB-231 Breast Adenocarcinoma cells. Cells and extracellular vesicles (EVs) from the resulting tumors were isolated. EVs were characterized by electron microscopy and Nanoparticle Tracking Analysis before total RNA isolation for comparative analysis with cellular RNA. Three biological replicates were analyzed in (technical) duplicate.

2015-03-05 | E-GEOD-66488 | biostudies-arrayexpress

RNASeq of HEK293 suspension cell-derived sEVs treated with a 72 h hyperthermic shift to 40°C versus untreated (37°C) controls

Project description:Experiment aimed at understanding the compositional changes of small extracellular vesicles (sEVs) derived from cells grown under hyperthermic conditions. Human embryonic kidney (HEK293) cells were cultured 48 h under normal conditions (37°C/140 rpm/5% CO2) before being subjected to a 72 h, 40°C temperature shift. sEVs were then isolated from the supernatant via tangential flow filtration (TFF) and size exclusion chromatography (SEC)

2023-08-18 | E-MTAB-13285 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data