| Literature DB >> 30873152 |
Andrey Turchinovich1,2, Oxana Drapkina3, Alexander Tonevitsky4,5,6.
Abstract
Exosomes and microvesicles are two major categories of extracellular vesicles (EVs) released by almost all cell types and are highly abundant in biological fluids. Both the molecular composition of EVs and their release are thought to be strictly regulated by external stimuli. Multiple studies have consistently demonstrated that EVs transfer proteins, lipids and RNA between various cell types, thus mediating intercellular communication, and signaling. Importantly, small non-coding RNAs within EVs are thought to be major contributors to the molecular events occurring in the recipient cell. Furthermore, RNA cargo in exosomes and microvesicles could hold tremendous potential as non-invasive biomarkers for multiple disorders, including pathologies of the immune system. This mini-review is aimed to provide the state-of-the-art in the EVs-associated RNA transcriptome field, as well as the comprehensive analysis of previous studies characterizing RNA content within EVs released by various cells using next-generation sequencing. Finally, we highlight the technical challenges associated with obtaining pure EVs and deep sequencing of the EV-associated RNAs.Entities:
Keywords: apoptotic bodies; circulating RNA; exosomes; extracellular vesicle (EV); microvesicles; next generation sequencing
Mesh:
Substances:
Year: 2019 PMID: 30873152 PMCID: PMC6404625 DOI: 10.3389/fimmu.2019.00202
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Figure 1Extracellular membrane vesicles. (A) The mechanisms of generation, size distribution, and common protein markers of different EVs types; (B) Different populations of EVs could be released depending on the side of the plasma membrane of a polar cell.
The reports demonstrating a transcriptome content of the EVs using deep sequencing.
| ( | Co-cultures of dendritic and T-cells | DUC (S10 –> P100) | EXOs & small MVs | Small RNA-seq (Illumina) | Exons (6.7%) incl. small ncRNA (0.49%), introns (19.4%), genomic repeats (27.4%); |
| ( | GT1-7 cells | DUC (S10 + 0.2 μm filtration –> P100) | EXOs & small MVs | Small RNA-seq (SOLID) | Genomic repeats (~50%), mRNA & ncRNA (~33%), small ncRNA (~15%), rRNA (~0.5%); |
| ( | HEK293T cells | DUC (S2 –> P100) | EXOs, MVs & ABs | Small RNA-seq (Illumina) for miRNA only | Various miRNAs |
| ( | Human plasma | Precipitation (ExoQuick) | EXOs & MVs | Small RNA-seq (Illumina) | miRNA (76.20%), rRNA (9.16%), DNA (5.63%), lncRNA (3.36%), mRNA (2.11%), piRNA (1.31%), tRNA |
| ( | Human saliva | UF (100 kDa) + GF | EXOs & small MVs | Small RNA-seq (Illumina) | miRNA (51-58%), rest: piRNA, snoRNA, genomic repeats |
| ( | MDA-MB-231, | DUC (S17 –> P100) | EXOs & small MVs | Total RNA-seq (Ion Torrent) | rRNA (~97%), protein coding (~1%), ncRNA (~1%) |
| ( | U251 cells | DC (S1.8 –> P18) | Large MVs & ABs | Small RNA-seq (SOLID) | miRNA (38.7%), genomic repeats (>20%), rest: tRNA, vault RNA, miscRNA, intergenic and intronic |
| ( | Human urine | DUC (S17 –> P200) | EXOs & small MVs | Small RNA-seq (Ion Torrent) | miRNA (35%), protein coding (3%), snRNA (0.02%), snoRNA (0.04%), lncRNA (0.19%), other non- coding RNAs (61%) |
| ( | Human urine | DUC (S17 –> P118) | EXOs & small MVs | Total RNA-seq (Illumina) | rRNA (87%), protein coding (4.6%), ncRNA and genomic repeats (6.1%), mtRNA (0.1%) |
| ( | Human mesenchymal stem cells | DUC (S10 –> P70) | EXOs & MVs | Small RNA-seq (Illumina) | tRNAs (23-50%), genomic repeats (17-40%), miRNA (2-5%), snoRNA (<0.6%), rest: miscRNA, rRNA, protein coding, snRNA, pseudogenes, mtRNA |
| ( | HMEC-1 cells | DUC (S10 –> P100) + SDG | EXOs & small MVs | Small RNA-seq (Illumina) | miRNA (~80%), Y-RNA (~14%), mRNA (~1.5%), mtRNA (~1%), lncRNAs (~0.8%), vault RNA (~0.2%), other ncRNA (<0.1%) |
| ( | MCF-7, MCF-10A cells | DC (S2 –> P16) | Large MVs & ABs | Small RNA-seq (Illumina) | Enriched in rRNA, Y-RNA, vault RNA, tRNA halves, much less miRNAs (<1%) |
| ( | MML-1 cells | DC (S0.3 –> P2) | ABs | Small RNA-seq (Ion Torrent) | ABs: 3.3-6.5% miRNAs, rest: snRNA, snoRNA, mtRNA, Y-RNA, vault RNA |
| ( | HMC-1, TF-1 cells | DUC (S16.5 –> P120) + SDG | EXOs & small MVs | Total RNA-seq and smRNA-seq (Illumina) | Total RNA-seq HD: protein coding (~75%), non-coding RNA (~25%); |
| ( | MKN45, SGC7901, NCI-N87, AGS, GES-1 cells | DUC (S2 –> P110) | EXOs, MVs & ABs | Small RNA-seq (Illumina) | miRNA (22-38%), rRNA (0.6-21%), snRNA (0.6-13%), rest: Y-RNA, piRNA, snoRNA, tRNA |
| ( | HuH7, Hep3B, HepG2, HuH6 cells | DUC (S16 –> P120) | EXOs & small MVs | Total RNA-seq & small RNA-seq (SOLID) | Total RNA-seq: rRNA (32-66%), genomic repeats (15-44%), transcriptome (11-25%); Small RNA-seq: rRNA (16-54%), genomic repeats (24-40%), transcriptome (24-51%) |
| ( | U87 cells | DUC (S10 –> P100) | EXOs & small MVs | Exome RNA-seq (Illumina) | Various mRNAs |
| ( | HEK293T, RD4, C2C12, Neuro2a, C17.2 cells | DUC (S1.5 + 0.2 μm filtration –> P110) | EXOs & small MVs | Small RNA-seq (Illumina) | rRNA (~60%), small ncRNA (~22%), rest: tRNAs, protein coding, Y-RNA, miscRNA; |
S, supernatant obtained after centrifugation at the corresponding g (in thousands); P, pellet obtained after centrifugation at the corresponding g (in thousands); DC, differential centrifugation; DUC, differential ultracentrifugation; SDG, sucrose density gradient ultracentrifugation; UF, ultrafiltration; GF, gel-filtration; EXOs, exosomes; MVs, microvesicles; ABs, apoptotic bodies.