RNA packaging into extracellular vesicles: An orchestra of RNA-binding proteins?

Abstract

Extracellular vesicles (EVs) are heterogeneous membranous particles released from the cells through different biogenetic and secretory mechanisms. We now conceive EVs as shuttles mediating cellular communication, carrying a variety of molecules resulting from intracellular homeostatic mechanisms. The RNA is a widely detected cargo and, impressively, a recognized functional intermediate that elects EVs as modulators of cancer cell phenotypes, determinants of disease spreading, cell surrogates in regenerative medicine, and a source for non-invasive molecular diagnostics. The mechanistic elucidation of the intracellular events responsible for the engagement of RNA into EVs will significantly improve the comprehension and possibly the prediction of EV "quality" in association with cell physiology. Interestingly, the application of multidisciplinary approaches, including biochemical as well as cell-based and computational strategies, is increasingly revealing an active RNA-packaging process implicating RNA-binding proteins (RBPs) in the sorting of coding and non-coding RNAs. In this review, we provide a comprehensive view of RBPs recently emerging as part of the EV biology, considering the scenarios where: (i) individual RBPs were detected in EVs along with their RNA substrates, (ii) RBPs were detected in EVs with inferred RNA targets, and (iii) EV-transcripts were found to harbour sequence motifs mirroring the activity of RBPs. Proteins so far identified are members of the hnRNP family (hnRNPA2B1, hnRNPC1, hnRNPG, hnRNPH1, hnRNPK, and hnRNPQ), as well as YBX1, HuR, AGO2, IGF2BP1, MEX3C, ANXA2, ALIX, NCL, FUS, TDP-43, MVP, LIN28, SRP9/14, QKI, and TERT. We describe the RBPs based on protein domain features, current knowledge on the association with human diseases, recognition of RNA consensus motifs, and the need to clarify the functional significance in different cellular contexts. We also summarize data on previously identified RBP inhibitor small molecules that could also be introduced in EV research as potential modulators of vesicular RNA sorting.

Keywords: EVs; RBPs; RNA; RNA consensus; RNA‐binding proteins; extracellular vesicles; inhibitors; protein domains.

FIGURE 1

RBPs identified in association with EVs and principal protein domain features. Secondary structures were recognized using primary sequence analysis by ProScan. RRM (RNA recognition motif), GLY_RICH (Glycine‐rich region profile) KH_TY (hnTNP K Homology domain type 1), ZF_RANBP2_2 (Zinc finger RanBP2 type profile), CSD_2 (Cold‐shock domain profile), ZF_CCHC (Zinc finger CCHC‐type profile), ANNEXIN_2 (Annexin repeat profile), BRO1 (BRO1 domain profile), PAZ (PAZ domain profile), PIWI (Piwi domain profile), RT_POL (Reverse transcriptase catalytic domain profile). QKI protein domains were not detected in ProScan