Characterization of protein, long noncoding RNA and microRNA signatures in extracellular vesicles derived from resting and degranulated mast cells

Abstract

Mast cells (MCs) are known to participate in a variety of patho-physiological processes depending largely on the intragranular mediators and the production of cytokines and chemokines during degranulation. Recently, extracellular vesicles (EVs) have been implicated important functions for MCs, but the components of MC-derived EVs have not yet been well-characterized. In this study, we aimed to identify signatures of proteins, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) in EVs derived from resting (Rest-EV) and degranulated (Sti-EV) MCs by differential ultracentrifugation. Using tandem mass tag (TMT)-based quantitative proteomics technology and RNA sequencing, we identified a total of 1988 proteins, 397 lncRNAs, and 272 miRNAs in Rest-EV and Sti-EV. The proteins include common EVs markers (cytoskeletal proteins), MCs markers (FcεRI and tryptase), and some preformed MCs mediators (lysosomal enzymes) as well. The global expression profiles of lncRNAs and miRNAs identified, for the first time, from Rest-EV and Sti-EV, strongly suggest a potential regulatory function of MC-derived EVs. We have also performed Western blotting and qRT-PCR analysis to further verify some of the proteins, lncRNAs, and miRNAs identified from Rest-EV and Sti-EV. Our findings will help to elucidate the functions of MC-derived EVs, and provide a reference dataset for future translational studies involving MC-derived EVs.

Long non-coding RNAs in brain tumors: roles and potential as therapeutic targets

“…Among the ncRNAs, diverse biological functions of lncRNAs have been identified, including in tumor biology, such as modulation of transcription and translation by acting as transcription factors, splicing of mRNA, modification of chromatin, interaction of ribosomes, sponging with miRNA, degradation of mRNAs, scaffolding of protein interactions, and trafficking of transcription factors [ 172 ]. Recently, several remarkable studies reported the relation of lncRNAs and EVs, which translocate the DNA, RNA, proteins, and lipids to other cells, resulting in diverse phenotypic responses that promote functional modulation of cellular activity in recipient cells [ 173 , 174 ]. Furthermore, lncRNAs and EVs are closely related with various diseases.…”

Identification and Comparison of Hyperglycemia-Induced Extracellular Vesicle Transcriptome in Different Mouse Stem Cells

“…In addition to mRNAs, ncRNAs including miRNAs and lncRNAs without protein coding potential have gained a lot of interest due to their regulatory roles in reparative processes of injured heart [ 32 , 38 , 39 , 40 ]. Moreover, RNA-sequencing data reveals that ncRNAs are selectively sorted into exosomes under stimulation [ 41 , 42 ]. Intensive studies have demonstrated that miRNAs enriched in stem/progenitor cell-derived EVs facilitate cardiac repair post-MI [ 32 , 43 , 44 ].…”

H3 relaxin protects against calcium oxalate crystal‐induced renal inflammatory pyroptosis

“…The DEPs were then annotated using the Database for Annotation, Visualization and Integrated Discovery (DAVID; https://david.ncifcrf.gov). Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analyses were further performed based on Fisher's exact test to map the DEPs 38,39 . The protein‐protein interaction (PPI) networks were predicted using STRING (https://string-db.org) and Cytoscape software 40 …”

“…The pooled TMT‐labelled peptides were then separated and analysed using a reversed‐phase high‐performance liquid chromatography and a nano‐UPLC (EASY‐nLC 1200) coupled to a Q‐Exactive mass spectrometer (Thermo Finnigan) as previously described 37 . The files were processed and quantitatively analysed using MaxQuant software (version 1.5.6.0), and the protein sequence database (UniProt, human, 2018, 10) was downloaded from UniProt 36,38 . Proteins with multiple relationships (ratio A/B > 1.25) and an adjusted P < .05 were defined as those with significant differences.…”