exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Abstract

Graphical Abstract Highlights d The exRNA Atlas provides access to human exRNA profiles and web-accessible tools d Atlas analysis reveals six exRNA cargo types present across five human biofluids d Five of the cargo types associate with specific vesicular and non-vesicular carriers d These findings and resources empower studies of extracellular RNA communication An extracellular RNA atlas from five human biofluids (serum, plasma, cerebrospinal fluid, saliva, and urine) reveals six extracellular RNA cargo types, including both vesicular and nonvesicular carriers. SUMMARY To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously.To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

Influence of species and processing parameters on recovery and content of brain tissue-derived extracellular vesicles

“…The results, with slightly different composition of large and small bdEVs, suggested that not all small RNAs are uniformly loaded from cells into EVs. Consistent with other reports 13,[38][39][40][41][42] , we also found that fragments of rRNA and tRNA, were more abundant than miRNAs in EVs, even without employing ligation-dependent sequencing library preparation 43 . Although some publications have reported a higher miRNA proportion in EVs 44, 45 than in cells, our results suggested that mapped miRNA reads and diversity gradually decreased from brain homogenate to large EVs and then small EVs.…”

Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome

“…However, the contribution of dead cells to□exRNA□profiles is unclear. Although identification of RNAs actively and selectively released to the extracellular space can help to understand physiological communication circuits between nonadjacent cells, nonselective RNA release (derived from either live or dead cells) can provide cell- or tissue-specific extracellular signatures which can be identified, at least in theory, by deconvolution analysis 29 . However, it is reasonable to expect that those exRNAs that are not contained inside EVs would be rapidly degraded by extracellular RNases.…”

Extracellular Vesicles in Non-Small-Cell Lung Cancer: Functional Role and Involvement in Resistance to Targeted Treatment and Immunotherapy

“…In particular, extracellular miRNAs can have a primary role in cell-to-cell communication, gene expression regulation, and cell reprogramming of target cells, as well as the exploration of the mechanisms of their release in the body fluids, assuming that an escalating focus on these molecules in the course of the last 2 to 3 years continues [37]. Out of total cell-free biofluid RNA, small non-coding RNA species, including miRNAs, are the most abundant in circulation, and are co-purified with both small EVs and non-EV particles [20,38]. A fraction of the functional miRNAs found into the blood are thought to be passively released by dying cells as complexes with RNA-binding proteins (RBPs) or encapsulated within apoptotic bodies [39,40].…”

“…Protein-RNA complexes are necessary to protect circulating miRNAs from plasma RNAases, and AGO2, the same effector of miRNA-mediated silencing [41], can also guide the release in the circulation of a bunch of cellular non-EV associated miRNAs with active biological functions [42]. Cell-released miRNAs can also be transported in the plasma and delivered to recipient cells by other non-vesicular particles, like high-density lipoprotein (HDL) complexes and exomeres [38,43]. However, most of the cell-released miRNAs involved in the direct silencing of cellular mRNAs are selectively delivered to target cells by loading within small EVs [20,38].…”