Small-RNA sequencing of sEV isolated from plasma of astronauts
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PROVIDER: PRJNA795799 | ENA |
REPOSITORIES: ENA
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Project description:We sought to determine whether the spaceflight environment can induce alterations in small extracellular vesicles (sEV) smallRNA content and their utility as biomarkers. Using small RNA sequencing (sRNAseq), we evaluated the impact of the spaceflight environment on sEV miRNA content in peripheral blood (PB) plasma of 14 astronauts, who flew STS missions between 1998-2001. Samples were collected at three-time points:10 days before the launch (L-10), the day of return (R-0), and three days post-landing (R+3).
2022-01-12 | GSE193331 | GEO
Project description:snoRNA sequencing of sEV isolated from plasma of astronauts
| PRJNA822839 | ENA
Project description:This study aimed to determine whether the spaceflight-induced snoRNA changes in plasma extracellular vesicles (EV) and astronauts' peripheral blood mononuclear cells (PBMCs) can be utilized as potential biomarkers. Using unbiased small RNA sequencing, we evaluated the EV snoRNA changes in peripheral blood (PB) plasma of astronauts (n=5/group) who underwent median 12-day long Shuttle missions between 1998-2001. Using stringent cutoff (> log 2-fold change, FDR < 0.05), we detected 21 down-regulated snoRNAs and 9 upregulated in PB-EVs at three days after return (R+3) compared to ten days before launch (L-10). Our findings unveiled that spaceflight induced changes in EV and PBMCs snoRNA expression, thus suggesting snoRNAs may serve as novel biomarkers for monitoring astronauts' health.
2022-04-06 | GSE200079 | GEO
Project description:Compared with plasma sEV (Con-sEV) from control rats, plasma sEV (DM-sEV) from 8-week diabetic rats significantly induced cardiomyocyte apoptosis as evidenced by increased percentage of apoptotic cells and activity of pro-apoptotic protein caspase 3. The proapoptotic effect of DM-sEV was blunted by RNase but not proteinase K, suggesting that DM-sEV exerted the cardiotoxic effects mainly through their contained RNAs. Increasing evidence suggests that miRNAs are the most important molecules by which sEV regulate recipient cell function. To identify the sEV-containing specific miRNAs responsible for the effects, Con-sEV and DM-sEV were subjected to miRNA sequencing.
2023-09-24 | GSE243560 | GEO
Project description:Purpose: The aim of this study is to compare the plasma miRNA profile between healthy control and sepsis patients Methods: Plasma from healthy control and sepsis patients were used in the study. Total RNA was isolated from equal volume of plasma using Trizol LS. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform.
2020-05-04 | GSE149764 | GEO
Project description:Label-free proteome analysis of small extracellular vesicles (sEV) derived from WM9 cells expressing different HRS mutants: wild type (HRSWT), phospho-deficient (HRSS345A), and phospho-mimetic mutant HRS (HRSS345D).
2022-02-16 | MSV000088846 | MassIVE
Project description:We report the sequencing of small RNAs present in the plasma of three normal subjects. In addition to microRNAs we identified abundant non-human small RNA sequences. The organisms from which these were derived were identified by BLAST searches with contigs assembled from the short sequences. The taxonomic profiles were very consistent between individuals, including plants and microbes reported previously in the microbiome, but in proportions distinct from other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Most reads mapped to rRNA sequences and the presence of specific common sequences was confirmed by RT-PCR. In addition, extremely abundant small RNAs derived from human Y RNAs were detected. We conclude that a characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The origin and potential function of these molecules remains to be determined, but the specific profile is likely to reflect health status. This facile test has immense potential to provide biomarkers for the diagnosis and prognosis of human disease. The profile of small RNAs present in the plasma of three normal subjects was determined
2014-09-29 | E-GEOD-52981 | biostudies-arrayexpress
Project description:Pancreatic ductal adenocarcinoma (PDAC) has a high fatality rate, mainly due to its asymptomatic nature until late-stage disease and therefore delayed diagnosis that leads to a lack of timely treatment intervention. Consequently, there is a significant need for better methods to screen populations that are at high risk of developing PDAC. Such advances would result in earlier diagnosis, more treatment options, and ultimately better outcomes for patients. Several recent studies have applied the concept of liquid biopsy, which is the sampling of a biofluid (such as blood plasma) for the presence of disease biomarkers, to develop screening approaches for PDAC; several of these studies have focused on analysis of extracellular vesicles (EVs) and their cargoes. While these studies have identified many potential biomarkers for PDAC that are present within EVs, their application to clinical practice is hindered by the lack of a robust, reproducible method for EV isolation and analysis that is amenable to a clinical setting. Our previous research has shown that the Vn96 synthetic peptide is indeed a robust and reproducible method for EV isolation that has the potential to be used in a clinical setting. We have therefore chosen to investigate the utility of the Vn96 synthetic peptide for this isolation of EVs from human plasma and the subsequent detection of small RNA biomarkers of PDAC by Next-generation sequencing (NGS) analysis. We find that analysis of small RNA from Vn96-isolated EVs permits the robust discrimination of PDAC patients from non-affected individuals. Moreover, analyses of all small RNA species, miRNAs, and lncRNAs are most effective at segregating PDAC patients from non-affected individuals. We further identified 34 chromosomal regions that encode small RNAs whose differential expression in Vn96-isolated EVs strongly distinguishes PDAC patients from non-affected individuals. Several of the identified small RNA biomarkers have been previously associated with and/or characterized in PDAC, indicating the validity of our findings, whereas other identified small RNA biomarkers may have novel roles in PDAC or cancer in general. Overall, our results provide a basis for a clinically-amendable detection and/or screening strategy for PDAC using a liquid biopsy approach that relies on Vn96-mediated isolation of EVs from plasma.
2023-06-08 | GSE221185 | GEO
Project description:High-throughput sequencing of the miRNAs present in plasma of COVID-19 patients at an early stage of the disease including non-SARS-CoV2 infected patients. This study allowed us to identify and functionally characterize human miRNAs associated with a worse evolution of the disease and a greater mortality. Samples were collected at hospital entry or within the first days after hospitalization and before treatment with immunotherapy for IL6 (e.g. Tocilizumab), interferon beta, corticoids and ribavirin, among others. Plasma samples were obtained from peripheral blood extracted in EDTA tubes after centrifugation. Total RNA, including small RNAs, was isolated from 400μl of plasma with the miRNeasy Serum Plasma Advanced kit (Qiagen). RNA quality and quantity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano Kit.
2022-04-03 | E-MTAB-10562 | biostudies-arrayexpress
Project description:Few studies have investigated the properties and function of small extracellular vesicles (sEV) derived from neurons under hypoxic conditions; these sEV represent potential new strategies for neuroprotection or neuroregeneration after ischemic stroke. We then performed gene expression profiling analysis using data obtained from RNA-seq of sEV derived from neurons under hypoxic conditions (HypEV) and those derived from neurons under normoxic conditions (NorEV).
2022-10-31 | GSE216866 | GEO