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ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types Present Across Human Biofluids

ABSTRACT: ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types Present Across Human Biofluids

PROVIDER: PRJNA510084 | ENA |

REPOSITORIES: ENA

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

Project description: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.

| S-EPMC6616370 | biostudies-literature

Assessment of RNA Isolation Kit Biases Toward Preferential Detection of exRNA Cargo Types

Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To determine whether different RNA isolation kits biased detection of certain exRNA cargo types, an integrative analysis was performed using pooled plasma and serum samples, where 10 different RNA isolation kits were applied.

2018-12-15 | GSE123865 | GEO

ExRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types Present Across Human Biofluids

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-15 | GSE123866 | GEO

Lipoprotein Particle (LPP) exRNA Profiles Isolated from Plasma

Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on lipoprotein particle (LPP) exRNA profiles obtained via sequential density ultracentrifugation (SD-UC) and fast protein liquid chromatography (FPLC).

2018-12-20 | GSE124131 | GEO

Ultracentifugation and nanoscale deterministic lateral displacement (nanoDLD) of samples for exRNA analysis

Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on those samples obtained via ultracentrifugation and nanoscale deterministic lateral displacement (nanoDLD).

2018-12-13 | GSE123736 | GEO

Assessment of RNA Isolation Kit Biases Toward Preferential Detection of exRNA Cargo Types

Project description:Assessment of RNA Isolation Kit Biases Toward Preferential Detection of exRNA Cargo Types

| PRJNA510086 | ENA

Physically Isolated OptiPrep (TM) Fractions for exRNA Analysis

Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. In order to detect differences in density between cargo types, cushioned density gradient ultracentrifugation (C-DGUC) of serum and plasma was performed using OptiPrem (TM) density gradient.

2018-12-15 | GSE123864 | GEO

Small RNA sequencing across diverse biofluids identifies optimal methods for exRNA isolation

Project description:Small RNA sequencing across diverse biofluids identifies optimal methods for exRNA isolation

| PRJNA671225 | ENA

Small RNA sequencing across diverse biofluids identifies optimal methods for exRNA isolation

Project description:Small RNA sequencing across diverse biofluids identifies optimal methods for exRNA isolation

| PRJNA671227 | ENA

Comparability of the small RNA secretome across human biofluids concomitantly collected from healthy adults

Project description:Small extracellular vesicles (sEV) are nano-sized (40-150 nm), membrane-encapsulated vesicles that are released by malignant or pathologic and non-pathologic cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA) and other small non-coding RNA (ncRNA), that can alter the phenotype of recipient cells. sEV are present in essentially all extracellular biofluids, including serum, urine and saliva, and offer a new avenue for discovery and development of novel biomarkers of various disease states and exposures. The objective of this study was to determine the similarities and differences between sEV ncRNA derived from saliva, serum and urine, as well as cell-free ncRNA from serum. Saliva, urine and serum were concomitantly collected from 4 healthy donors, and sEV were isolated from each respective biofluid, along with cfRNA from serum. sEVs were isolated from the respective biofluids via differential ultracentrifugation. Small RNA-sequencing was performed on each sample, and cluster analysis was performed based on ncRNA profiles. While some similarities existed in terms of sEV ncRNA cargo across biofluids, there are also notable differences in ncRNA class and ncRNA secretion, with each sEVs in each biofluid bearing a unique ncRNA profile. We conclude that sEV ncRNA cargo varies according to biofluid, so thus should be carefully selected and interpreted when designing translational or epidemiological studies.

2020-02-25 | GSE122621 | GEO

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