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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-Seq of Tissue, Plasma and Urinary Extracellular Vesicles of Prostate Cancer patients

ABSTRACT: We performed RNA-Seq analysis of plasma and urinary EVs collected before and after radical prostatectomy, and matched tumor and normal prostate tissues of 10 patients with prostate cancer. To identify putative cancer-derived RNA biomarkers, we searched for RNAs that were overexpressed in tumor as compared to normal tissues, present in the pre-operation EVs and decreased in the post-operation EVs in each RNA biotype.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Pawel Zayakin

PROVIDER: E-MTAB-11910 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA-Seq of Tissue, Feces and Plasma Extracellular Vesicles of Gastric Cancer patients at the time of diagnosis and after the surgery

Project description:In the current study, we performed deep sequencing analysis of the RNA cargo of plasma and fecal EVs collected at the time of diagnosis, after the surgery and matched tumor and normal tissues from 23 patients with gastric cancer, and 15 cancer-free donors.

2023-04-01 | E-MTAB-12013 | biostudies-arrayexpress

RNA-Seq of tissue and plasma extracellular vesicles of breast cancer patients at the time of diagnosis and after the breast surgery

Project description:In the current study, we performed deep sequencing analysis of the RNA cargo of plasma EVs collected at the time of diagnosis, during and after the NAC and up to 18 months after the surgery and matched tumor and normal tissues from 35 patients with locally advanced BC, and 30 cancer-free females.

2022-10-24 | E-MTAB-12014 | biostudies-arrayexpress

RNA-Seq of effects of exercise-induced Extracellular Vesicles on an F344 rat (Rattus norvegicus) model of forced running wheel exercise

Project description:n total, 16 7-week-old male F344 rats were subjected to model regular exercise and sedentary lifestyle. In the second week after arrival and acclimatization to the reversed light/dark cycle, rats were introduced to the forced running wheel without a specific running mode. It was followed by a 12-day training phase for all 16 experimental animals (started at 9 weeks of age) by gradually increasing the running speed and duration. During the training phase, 8 best performers were selected for the runner group while the remaining 8 rats were assigned to the sedentary group. The regular forced running exercise phase for the runner group lasted for 5 weeks in total, including 4 weeks of regular running. After 4 weeks of regular exercise, rats underwent brief anesthesia and of blood from the tail vein were taken. This step was repeated for the same animals immediately after 1h of running. On the same day, a blood sample was collected from the sedentary rats following the same protocol. Plasma was collected and immediately frozen for further EV isolation. EVs were isolated from rat plasma by size exclusion chromatography. RNA libraries were constructed using CleanTag® Small RNA Library Prep Kit (Trilink Biotechnologies, USA) and sequenced on Illumina NextSeq500 instrument using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles).

2021-12-28 | E-MTAB-11020 | 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.

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Role of miRNAs in acute kidney injury recovery induced by mesenchymal stromal cells and derived extracellular vesicles.

Project description:Phenotypic changes induced by extracellular vesicles (EVs) have been implicated in the recovery of acute kidney injury (AKI) induced by mesenchymal stromal cells (MSCs). miRNAs are potential candidates for cell reprogramming towards a pro-regenerative phenotype. The aim of the present study was to evaluate whether miRNA de-regulation inhibits the regenerative potential of MSCs and derived-EVs in a model of glycerol-induced AKI in SCID mice. For this purpose, we generated MSCs depleted of Drosha, a critical enzyme of miRNA maturation, to alter miRNA expression within MSCs and EVs. Drosha knock-down MSCs (MSC-Dsh) maintained the phenotype and differentiation capacity. They produced EVs that did not differ from those of wild type cells in quantity, surface molecule expression and internalization within renal tubular epithelial cells. However, EVs derived from MSC-Dsh (EV-Dsh) showed global down-regulation of miRNAs. Whereas, wild type MSCs and derived EVs were able to induce morphological and functional recovery in AKI, MSC-Dsh and EV-Dsh were ineffective. RNA sequencing analysis showed that genes deregulated in the kidney of AKI mice were restored by treatment with MSCs and EVs but not by MSC-Dsh and EV-Dsh. Gene Ontology analysis showed that down-regulated genes in AKI were associated with fatty acid metabolism. The up-regulated genes in AKI were involved in inflammation, ECM-receptor interaction and cell adhesion molecules. These alterations were reverted by treatment with wild type MSCs and EVs, but not by the Drosha counterparts. In conclusion, miRNA depletion in MSCs and EVs significantly reduced their intrinsic regenerative potential in AKI, suggesting a critical role of miRNAs. RNA-seq

2015-05-07 | E-GEOD-59958 | 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

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

Prostate Cancer (PRC) training cohort for small RNA characterization

Project description:RNA sequencing study on prostate cancer (PRC) cohort for small RNA characterization across biofluids, tissue types and isolation techniques.

2022-06-01 | E-MTAB-8529 | biostudies-arrayexpress

Characterization and Small RNA Content of Extracellular Vesicles in Follicular Fluid of Developing Bovine Antral Follicles

Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle. Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles

2016-02-09 | E-GEOD-74879 | biostudies-arrayexpress

Massive sequencing of hybrid DNA obtained by DNA:RNA immunoprecipitation (DRIP) in extracellular microvesicles (MV) produced by HeLa cells (using S9.6 antibody)

Project description:Hybrid (Bound) and non-hybrid (Unbound) DNA from Hela EV was isolated using DRIP procedure as follows. Between 1-5μg of nucleic acid DNA from EVs (DNase0 treated) was incubated overnight with 1μg of anti-DNA-RNA Hybrid (S9.6) antibody (KeraFast) under rotation at 4°C in 500μl of binding buffer (10mM NaPO4 pH 7.0, 140 mM NaCl, 0.05% Triton X-100). The following day, 25μl of A/G magnetic beads (Pierce™) were washed twice in 500μl of binding buffer (30' min each wash) and added for 2h at room temperature under rotation to the S9.6+nucleic acid complex. The nucleic acids bound to the S9.6 antibody (Hybrid fraction or Bound) were separated from those unbound (Non-Hybrid or Unbound) by using a magnetic rack (which captured the Bead+Hybrid fraction). 500μl of the unbound fraction (bead-free) were transferred into a new 1.5ml tube and collected for further analysis. The Bead+Hybrid fraction was washed twice in 250μl binding buffer for 15' min at room temperature under rotation. The hybrids were then eluted with 250μl of elution buffer (50mM TRIS pH 8.0, 10mM EDTA, 0.5% SDS) for 15' min at room temperature under rotation. The elution step was repeated twice to make sure that all the hybrid molecules were collected. As a control of all there experiments to make sure, we were isolating and precipitating Hybrid DNA:RNA molecules, samples were also pre-treated with RNaseH1 (RNaseH), which degrades the RNA filament only when present in the hybrid structure.

2023-03-30 | E-MTAB-9634 | biostudies-arrayexpress

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