Title: Profiling Small RNA from Brain Extracellular Vesicles in Individuals with Depression
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1075092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27928600.fastq.gz | Fastqsanger.gz | |||
| SRR27928601.fastq.gz | Fastqsanger.gz | |||
| SRR27928562.fastq.gz | Fastqsanger.gz | |||
| SRR27928563.fastq.gz | Fastqsanger.gz | |||
| SRR27928564.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Title: Profiling Small RNA from Brain Extracellular Vesicles in Individuals with Depression [NovaSeq]
| PRJNA1075094 | ENA
Project description:Major depressive disorder (MDD) is a leading cause of disability with significant mortality risk. Despite progress in our understanding of the etiology of MDD, the underlying molecular changes in the brain remain poorly understood. Extracellular vesicles (EVs) are lipid-bound particles that can reflect the molecular signatures of the tissue of origin. We aimed to optimize a streamlined EV isolation protocol from post-mortem brain tissue and to determine whether EV RNA cargo, particularly microRNAs (miRNAs) have an MDD-specific profile. EVs were isolated from post-mortem human brain tissue. Quality was assessed using western blots, transmission electron microscopy, and microfluidic resistive pulse sensing. EV RNA was extracted and sequenced on Illumina platforms. Functional follow up was performed in silico. Quality assessment showed an enrichment of EV markers, as well as a size distribution of 30-200 nm in diameter, and no contamination with cellular debris. Small RNA profiling indicated the presence of several RNA biotypes, with miRNAs and transfer RNAs (tRNAs) being the most prominent. Exploring miRNA levels between groups revealed decreased expression of miR-92a-3p and miR-129-5p, which was validated by qPCR and was specific to EVs and not seen in bulk tissue. Finally, in silico functional analyses indicate potential roles for these two miRNAs in neurotransmission and synaptic plasticity. We provide a streamlined isolation protocol that yields EVs of high quality that are suitable for molecular follow up. Our findings warrant future investigations into brain EV miRNA dysregulation in MDD.
2024-03-20 | GSE255478 | GEO
Project description:Major depressive disorder (MDD) is a leading cause of disability with significant mortality risk. Despite progress in our understanding of the etiology of MDD, the underlying molecular changes in the brain remain poorly understood. Extracellular vesicles (EVs) are lipid-bound particles that can reflect the molecular signatures of the tissue of origin. We aimed to optimize a streamlined EV isolation protocol from post-mortem brain tissue and to determine whether EV RNA cargo, particularly microRNAs (miRNAs) have an MDD-specific profile. EVs were isolated from post-mortem human brain tissue. Quality was assessed using western blots, transmission electron microscopy, and microfluidic resistive pulse sensing. EV RNA was extracted and sequenced on Illumina platforms. Functional follow up was performed in silico. Quality assessment showed an enrichment of EV markers, as well as a size distribution of 30-200 nm in diameter, and no contamination with cellular debris. Small RNA profiling indicated the presence of several RNA biotypes, with miRNAs and transfer RNAs (tRNAs) being the most prominent. Exploring miRNA levels between groups revealed decreased expression of miR-92a-3p and miR-129-5p, which was validated by qPCR and was specific to EVs and not seen in bulk tissue. Finally, in silico functional analyses indicate potential roles for these two miRNAs in neurotransmission and synaptic plasticity. We provide a streamlined isolation protocol that yields EVs of high quality that are suitable for molecular follow up. Our findings warrant future investigations into brain EV miRNA dysregulation in MDD.
2024-03-20 | GSE255480 | GEO
Project description:Background: There is some evidence demonstrating the effect of psychological interventions in improvements in health biological parameters. To best of our knowledge, no study had addressed the impact of any psychological intervention on extracellular vesicles. In addition, Mindfulness-Based Cognitive Therapy (MBCT) and Emotion Focused Therapy for Cancer Recovery (EFT-CR) in the group have never been explored regarding extracellular vesicles and the effectiveness of these was not compared yet.
Objectives:
1. To explore and compare the effect of MBCT and EFT-CR on biological parameters and psychological variables in distressed people who have had breast, prostate and colorectal cancer;
2. In addition, we will explore the acceptability through recruitment and retention rates of MBCT and EFT-CR in group and evaluate whether these interventions are appropriate for a larger clinical trial.
Methods: The design of this study is a parallel randomized controlled trial. Participants will be randomized into MBCT, EFT-CR or usual care. Outcome measures will be assessed before, at the end of the intervention (8 weeks) and follow-ups (24 and 52 weeks from the baseline moment).
Hypotheses: The researchers expected that both interventions will have an effect on extracellular vesicles and other study biomarkers as well as improvements in psychological outcomes, compared to treatment as usual (TAU) group. Regarding the comparative effectiveness, we did not have evidence to hypothesize which one of the interventions will be superior in both biological (extracellular vesicles) and psychological outcomes.
Contribution for practice: The results of this preliminary study would permit to know if there are benefits of these psychological interventions on changes in extracellular vesicles and on psychological outcomes related to health. In addition, this study will permit to determine the acceptability of conducting a larger randomized controlled trial.
| 2332322 | ecrin-mdr-crc
Project description:To further investigate the molecular mechanisms by which EVs mediated the abnormal localization of tight junction proteins and adherence junction protein, we performed miRNA microarray analysis of extracellular vesicles isolated from breast cancer cells. miRNA expression in extracellular vesicles was collected from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.
2015-04-02 | E-GEOD-63445 | biostudies-arrayexpress
Project description:Similar to bacterial proteins that are targeted to distinct macrophages organelles via extracellular vesicles, we propose that these vesicles also traffic small RNAs to modulate specific host factors. To test this, we aim to sequence extracellular vesicle derived sRNA, and whole bacterial small RNAs to determine selectivity, and to identify their bacterial and mammalian targets (Experimental Plan in Table-1). For this we will collect highly purified vesicles from N. gonorrhoeae (strain MS11A). We will also treat mouse derived primary macrophages with extracellular vesicles and compare their RNA response to untreated macrophages (Table-2). This will provide novel insights into how macrophages respond to N. gonorrhoeae infections. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-03-01 | E-ERAD-439 | biostudies-arrayexpress
Project description:Extracellular vesicles Raw sequence reads
| PRJNA816091 | ENA
Project description:comparison miRNA content between extracellular vesicles from AAV-transduced or intact cells
2021-08-07 | E-MTAB-10858 | biostudies-arrayexpress
Project description:A growing body of evidence in mammalian cells indicates that secreted vesicles can be used to mediate intercellular communication processes by transferring various bioactive molecules, including mRNAs and microRNAs. Based on these findings, we decided to analyze whether T. cruzi-derived extracellular vesicles contain RNA molecules and performed a deep sequencing and genome-wide analysis of a size-fractioned cDNA library (16M-bM-^@M-^S40 nt) from extracellular vesicles secreted by noninfective epimastigote and infective metacyclic trypomastigote forms. Our data show that the small RNAs contained in these extracellular vesicles originate from multiple sources, including tRNAs. In addition, our results reveal that the variety and expression of small RNAs are different between parasite stages, suggesting diverse functions. Taken together, these observations call attention to the potential regulatory functions that these RNAs might play once transferred between parasites and/or to mammalian host cells. Small RNAs profiles (16-40 nt) of epimastigote-derived extracellular vesicles, metacyclic trypomastigote-derived extracellular vesicles and metacyclic trypomastigote parental cells.
2014-07-15 | E-GEOD-54111 | biostudies-arrayexpress
Project description:Neural stem cell-derived extracellular vesicles (NSC-EVs) have emerged as promising candidates for neurological disease treatment through delivering bioactive cargoes with therapeutic effects, but their roles in major depressive disorder (MDD) remains poorly understood. Here, we collected NSC-EVs and showed these EVs penetrated the blood-brain-barrier and internalized by brain cells via intravenous injection. NSC-EVs alleviated chronic restraint stress (CRS)-induced depression-like behavioral and pathological alterations presumably through inhibiting inflammatory responses and excessive synaptic pruning of microglia. We next identified miR-16-5p as a key component of NSC-EVs responsible for their therapeutic effects by directly targeting Cxcr4 in microglia. We further demonstrated that either microglial Cxcr4 knockout or Cxcr4 inhibitors treatment significantly mitigated depression-like phenotypes of CRS mice. Thus, our findings suggest NSC-EVs as a novel therapeutic strategy and identified Cxcr4 a potential therapeutic target of MDD.
2025-10-25 | GSE292766 | GEO