Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative analysis of gut EVs from mice on high and low fat diet

ABSTRACT: Currently, it is an open question how gut senses metabolic alterations and whether this is transmitted to other tissues via EVs. Here, we observed that protein packaging in gut derived EVs (GDE) from a diet induced-prediabetic mouse mode, specifically small intestine, is increased in prediabetes. Proteins related to lipid metabolism and to oxidative stress management were more abundant in prediabetic GDE compared to healthy controls. Low-fat diet: A1 to A3 high-fat diet: A4 to A6

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Gut, Extracellular Vesicle

DISEASE(S): Type 2 Diabetes Mellitus

SUBMITTER: Rune Matthiesen

LAB HEAD: Rune Matthiesen

PROVIDER: PXD028338 | Pride | 2022-04-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	A1_1.mgf	Mgf
	A1_1.raw	Raw
	A1_1_PepInfo.txt	Txt
	A1_2.mgf	Mgf
	A1_2.raw	Raw

Items per page:

1 - 5 of 55

Publications

Messages from the Small Intestine Carried by Extracellular Vesicles in Prediabetes: A Proteomic Portrait.

Ferreira Inês I Machado de Oliveira Rita R Carvalho Ana Sofia AS Teshima Akiko A Beck Hans Christian HC Matthiesen Rune R Costa-Silva Bruno B Macedo Maria Paula MP

Journal of proteome research 20220309 4

Extracellular vesicles (EVs) mediate communication in physiological and pathological conditions. In the pathogenesis of type 2 diabetes, inter-organ communication plays an important role in its progress and metabolic surgery leads to its remission. Moreover, gut dysbiosis is emerging as a diabetogenic factor. However, it remains unclear how the gut senses metabolic alterations and whether this is transmitted to other tissues via EVs. Using a diet-induced prediabetic mouse model, we observed that ...[more]

PMID: 35263542

Similar Datasets

Human, bronchoalveolar lavage, extracellular vesicles

Project description:The aim of the project was to explore large extracellular vesicles capacity to seperate non lung cancer from lung cancer cases. A case control study of patients suspected for lung cancer (12 non lung cancer and 12 lung cancers). The raw files are labeled according to clinical status. Small and large extracellular vesicles were isolated by differential centrifugation. The proteome of full BAL, vesicle depleted BAL, small and large extracellular vesicles were characterized by LC-MS. Small extracellular vesicles were further analyzed by nanoparticle tracking analysis, Transmission electron microscopy and western blots.

2020-12-15 | PXD021988 | Pride

BAG6KO impacts extracellular vesicle mRNA cargo

Project description:The mRNA cargo of B-16V and B-16V-delta-BAG6 cells was sequenced with RNA seq.

2019-11-29 | E-MTAB-7123 | 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

Glioblastoma biomarkers in urinary extracellular vesicles reveal the potential for a ‘liquid gold’ biopsy

Project description:Background: Biomarkers that reflect glioblastoma tumour activity and treatment response are urgently needed to help guide clinical management, particularly for recurrent disease. As the urinary system is a major clearance route of circulating extracellular vesicles (EVs; 30-1000 nm nanoparticles) we explored whether sampling urinary-EVs could serve as a simple and non-invasive liquid biopsy approach for measuring glioblastoma-associated biomarkers. Methods: Fifty urine specimens (15-60 ml) were collected from 24 catheterised glioblastoma patients immediately prior to primary (n=17) and recurrence (n=7) surgeries, following gross total resection (n=9), and from age/gender-matched healthy participants (n=14). EVs isolated by differential ultracentrifugation were characterised and extracted proteomes were analysed by high-resolution data-independent acquisition liquid chromatography tandem mass spectrometry (DIA-LC-MS/MS). Results: Overall, 6857 proteins were confidently identified in urinary-EVs (q-value≤0.01), including 94 EV marker proteins. Glioblastoma-specific proteomic signatures were determined, and putative urinary-EV biomarkers corresponding to tumour burden and recurrence were identified (FC≥|2|, adjust p-val≤0.05, AUC>0.9). Conclusion: In-depth DIA-LC-MS/MS characterisation of urinary-EVs substantiates urine as a viable source of glioblastoma biomarkers. The promising ‘liquid gold’ biomarker panels described here warrant further investigation.

2024-04-18 | PXD046511 | Pride

Multiple myeloma-derived extracellular vesicles modulate the bone marrow immune microenvironment

Project description:One of the hallmarks of multiple myeloma (MM) is a permissive BM microenvironment. Increasing evidence suggest that cell-to-cell communication between myeloma and immune cells via tumor cell-derived extracellular vesicles (EV) plays a key role in the pathogenesis of MM. Hence, we aimed to explore BM immune alterations induced by MM-derived EV. For this, we inoculated immunocompetent BALB/cByJ mice with a myeloma cell line - MOPC315.BM -, inducing a MM phenotype. Upon tumor establishment, characterization of the BM microenvironment revealed the expression of both activation and suppressive markers by lymphocytes, such as Granzyme b and PD-1, respectively. In addition, conditioning of the animals with MOPC315.BM-derived EV, before transplantation of the MOPC315.BM tumor cells, did not anticipate the disease phenotype. However, it induced features of suppression in the BM milieu, such as an increase in PD-1 expression by CD4+ T cells. Overall, our findings reveal the involvement of MOPC315.BM-derived EV protein content as promoters of immune niche remodeling, strengthening the importance of assessing the mechanisms by which MM may impact the immune microenvironment.

2022-07-05 | PXD032934 | Pride

Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation

Project description:Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that Drosophila, like human cells release exosome-like EVs with diameter ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNA pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these extensive similarities suggest that EVs could also enable RNA-mediated intercellular communication in Drosophila. We performed RNA-seq on extracellular vesicles purified from of human and Drosophila cell line cultures. S2R+ and D17 Drosophila EVs were analyzed, along with human A431 and HepG2 EVs. No ribosomal RNA depletion or polyA selection was performed on EV samples. For comparative analyses, we also analyzed total cellular RNA from Drosophila D17 and human HepG2. Ribodepletion was performed on cellular samples.

2016-06-15 | E-GEOD-76173 | biostudies-arrayexpress

Cellular and extracellular vesicle RNA sequence for E-cadherin-RFP EMT reporter system expressing mouse breast cancer cell line Py2T during EMT/MET

Project description:Epithelial-mesenchymal transition (EMT) is a process by which epithelial cells lose cell-cell contact and gain cancer malignancy such as invasion, stemness, chemoresistance and metastasis. Reverse precess, mesenchymal-epithelial transition (MET) is also important for colonization. Extracellular vesicles (EVs) secreted from cancer cells are also important for cancer malignancy. To analyze RNAs from cells and EVs during EMT and MET, RNA sequencing was performed using E-cadherin-RFP/Py2T reporter system.

2020-12-31 | E-MTAB-9750 | biostudies-arrayexpress

Human iPSC-derived cardiomyocytes under hypoxia/normoxia, treated with bone marrow or cardiac stromal cell extracellular vesicles

Project description:RNA-seq was performed on cultured human induced pluripotent cell derived cardiomyocytes (iPSC-CMs). There are four groups, with three samples per group: H1,H2,H3. Negative control. Healthy, normoxic iPSC-CMs D1,D2,D3. Positive control. iPSCs cultured under hypoxic (0-1% O2) for 48h with 2% v/v PBS as vehicle control EV1,EV2,EV3. Treatment 1. iPSCs cultured under hypoxic (0-1% O2) for 48h, with cardiac stromal cell derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) EV21, EV23, EV24. Treatment 2 iPSCs cultured under hypoxic (0-1% O2) for 48h, with bone marrow mesenchymal stromal cell (BM-MSC) derived extracellular vesicles, provided at a dose of 67ng/µl (2% v/v) All EVs were isolated from cultured human cells using sequential centrifugation methods. Cells were cultured using commercial EV-depleted FBS to avoid contamination of bovine EVs. EVs were validated for CD81, CD9, ALIX positivity, and visualised by cryoEM. Particle to protein ratios were not different between cardiac and bone marrow EV isolates. Therefore EV doses were standardised so that the same dose by protein (67ng/µl) and EV number (~2,000 EVs per iPSC-CM) were added.

2024-10-02 | E-MTAB-13966 | biostudies-arrayexpress

The miRNAs high-throughput sequencing of extracellular vesicles derived from A549 cell lines treated with and without intermittent hypoxia

Project description:The miRNAs high-throughput sequencing for extracellular vesicles derived from A549 cell lines treated with and without intermittent hypoxia (EV-NA and EV-IH) were carried out. Three samples were processed for each group. The total RNA or purified sRNA fragment of the sample was extracted, and the 3 'and 5' connectors were successively connected to reverse transcription into cDNA, and then PCR amplification was performed. Then the target fragment library was recovered by glue cutting, and the qualified library was sequenced. Clean reads obtained by sequencing were compared with all mature miRNA sequences in miRDeep2 and miRBase. v22 database to obtain the structure, length and other information of miRNA and calculate its expression level.

2023-04-29 | E-MTAB-11838 | biostudies-arrayexpress

NanoString assays of miRNA in MCF7 and MCF10A cells and in extracellular vesicles (EVs) derived from these cells.

Project description:The goal of this study is to identify unique miRNA profiles of EVs from MCF7 and MCF10A cells that distinguish their cellular origin. 654 human mature miRNAs were analyzed in NanoString assays to identify miRNA with high abundance in MCF7 EVs and the greatest fold change for MCF7 EVs relative to MCF10A EVs.

2015-02-21 | E-GEOD-66165 | 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