Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26358883.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Macrophages are often classified into M1 ‘classical’ and M2 ‘alternatively-activated’ macrophages. Extracellular vesicles (EVs) are biomolecule carriers involved in cell-cell communication. Here, we provide a first insight into the complete small RNA cargo of human macrophage M1/M2 EVs. Methods: Monocyte-derived macrophages were polarised into M1 (GM-CSF+LPS+IFNγ) or M2 (M-CSF+IL-4+IL-13) and EVs isolated by size exclusion chromatography. EVs were characterised by nanoparticle tracking analysis, electron microscopy and ELISA. EV RNA samples were prepared for small RNA sequencing using Qiagen’s GIAseq small RNA Library Prep kit and sequenced on an Illumina NextSeq500, single end 75 bp. Functional enrichment analysis was performed using MIENTURNET, based on validated miR-target interactions from miRTarBase. Results: Many types of small non-coding RNAs were found in EVs from M1/M2 macrophages including miRNAs, isomiRs, tRNA fragments, piRNA, snRNA, snoRNA and yRNA fragments. Distinct differences were observed between M1 and M2 EVs, with higher relative abundance of miRNAs, and lower abundance of tRNA fragments in M1 EVs compared to M2 EVs. MicroRNA-target enrichment analysis identified several gene targets involved in gene expression and metabolic processes. Conclusions: M1 and M2 cells release EVs with distinct tRNA and miRNA cargo, which have the potential to contribute to the unique effect of these cell subsets on their microenvironment.
2022-12-07 | GSE207286 | GEO
Project description:The ubiquitin-proteasome system (UPS) is a key regulatory mechanism in plant immunity. Target proteins are labelled with ubiquitin chains that form distinct topological structures to modulate their activity and stability. Here, we identified ubiquitin-binding proteins (UBPs) that specifically interact with M1-, K48-, and K63-linked ubiquitin chains in response to SA or infection with the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm). Four-week-old plants were sprayed with 0.5 mM SA or inoculated with Psm ES4326, samples were harvested after 24 hours post-treatment. For the M1- and K48-linked ubiquitin chain pulldown assays, monoubiquitin (Ub) was used as a control. For the K63-linked ubiquitin chain pulldown, empty agarose beads (Beads) served as the control. In total three independent biological repeats were collected.
2026-02-12 | PXD071198 | Pride
Project description:Microvascular endothelial cells play important roles in sepsis-associated acute kidney injury (SA-AKI). In this study, we focused on microvascular microRNAs changes following SA-AKI to identify microRNAs as novel druggable targets and microvasculature-related early biomarkers of SA-AKI. Using small RNA sequencing we identified 40 differentially expressed microRNAs in the renal microvasculature in response to SA-AKI. While the induction of most microRNAs was restricted to a single microvascular compartment, miR-21-5p levels were increased across the renal microvasculature in both mice and humans following SA-AKI. Functional assessment in vitro revealed that inhibition of hsa-miR-21-5p exacerbated endothelial inflammatory activation, suggesting a protective role of this microRNA in endothelial cells. Furthermore, patients with SA-AKI exhibited elevated hsa-miR-21-5p levels in plasma compared with critically ill sepsis patients without AKI. These results highlight the potential of hsa-miR-21-5p and other microRNAs as therapeutic targets and biomarkers in SA-AKI.
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Project description:Asthma is a chronic lung disease with various clinical phenotypes, complicating its diagnosis and treatment. The micro-RNA (miRNA) profile of plasma-derived extracellular vesicles (EVs) may serve as potential circulating biomarkers for differentiating asthma phenotypes/endotypes. This study aims to characterize and compare the miRNA profiles in plasma-derived EVs across healthy controls (HC), non-severe asthmatics (NS), and severe asthmatics (SA). EVs were isolated from plasma samples of HC, NS, and SA, followed by physiochemical characterization and RNA isolation. Small RNA sequencing was performed, and differentially expressed (DE) miRNAs were identified through DESeq2 analysis. DE miRNAs and their predicted mRNA targets were identified using Ingenuity Pathway Analysis (IPA), and pathway enrichment was conducted using STRING DB and Enrichr. EVs from all groups were predominantly ~150-200 nm in size, with significantly higher EV counts in SA compared to HC and NS. miRNA expression analysis revealed unique and shared DE miRNAs across the three comparisons (HC vs. NS; HC vs. SA; NS vs. SA). A total of 16 unique DE miRNAs among these comparisons, between which in the NS vs. SA comparison, miR-515-3p positively correlates with lung function, and exacerbation and miR-133a-3p and miR-9-5p with ACT score. Target and pathway analyses from the NS vs. SA comparison indicated the enrichment of key pathways, including IL-4/IL-13, Th1, Th2, and Th17 cell differentiation, MAPK, PI3K-Akt, and receptor tyrosine kinase signaling. This study identified distinct miRNAs in plasma-derived EVs from NS vs. SA which could serve as potential circulating biomarkers for differentiating asthma severity.
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Project description:In this study, we have combined RNA-seq, Ribo-seq and shotgun proteomic analyses to identify and validate the expression of novel small proteins in Staphylococcus aureus.
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