Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

Alexander, Roger P.; Kitchen, Robert; Tosar, Juan Pablo; Roth, Matthew E.; Mestdagh, Pieter; Max, Klaas E.A.; Rozowsky, Joel; Kaczor‐Urbanowicz, Karolina Elżbieta; Chang, Justin; Balaj, Leonora; Losic, Bojan; Nostrand, Eric L. Van; LaPlante, Emily L.; Mateescu, Bogdan; White, Brian S.; Yu, Rongshan; Milosavljevic, A.; Stolovitzky, Gustavo; Spengler, Ryan M

doi:10.3389/fgene.2021.778416

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…The limitations encountered with sequencing technologies could be addressed through novel pipelines such as that reported by Amorim et al [ 22 ]. Ongoing collaborative work such as the Extracellular RNA Communication Consortium has made efforts to improve this and work towards strategies such as deconvolution to determine tRNA sources [ 80 ].…”

Section: Discussionmentioning

confidence: 99%

The Clinical Significance of Transfer RNAs Present in Extracellular Vesicles

Liu

Yang

Asim

et al. 2022

IJMS

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Extracellular vesicles (EVs) are important for intercellular signalling in multi-cellular organisms. However, the role of mature transfer RNAs (tRNAs) and tRNA fragments in EVs has yet to be characterised. This systematic review aimed to identify up-to-date literature on tRNAs present within human EVs and explores their potential clinical significance in health and disease. A comprehensive and systematic literature search was performed, and the study was conducted in accordance with PRISMA guidelines. Electronic databases MEDLINE and EMBASE were searched up until 1 January 2022. From 685 papers, 60 studies were identified for analysis. The majority of papers reviewed focussed on the role of EV tRNAs in cancers (31.7%), with numerous other conditions represented. Blood and cell lines were the most common EV sources, representing 85.9% of protocols used. EV isolation methods included most known methods, precipitation being the most common (49.3%). The proportion of EV tRNAs was highly variable, ranging between 0.04% to >95% depending on tissue source. EV tRNAs are present in a multitude of sources and show promise as disease markers in breast cancer, gastrointestinal cancers, and other diseases. EV tRNA research is an emerging field, with increasing numbers of papers highlighting novel methodologies for tRNA and tRNA fragment discovery.

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Section: Discussionmentioning

confidence: 99%

The Clinical Significance of Transfer RNAs Present in Extracellular Vesicles

Liu

Yang

Asim

et al. 2022

IJMS

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Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations

Miceli,

Chen,

Nose

et al. 2024

J of Extracellular Vesicle

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Extracellular vesicles (EVs) are heterogeneous entities secreted by cells into their microenvironment and systemic circulation. Circulating EVs carry functional small RNAs and other molecular footprints from their cell of origin, and thus have evident applications in liquid biopsy, therapeutics, and intercellular communication. Yet, the complete transcriptomic landscape of EVs is poorly characterized due to critical limitations including variable protocols used for EV‐RNA extraction, quality control, cDNA library preparation, sequencing technologies, and bioinformatic analyses. Consequently, there is a gap in knowledge and the need for a standardized approach in delineating EV‐RNAs. Here, we address these gaps by describing the following points by (1) focusing on the large canopy of the EVs and particles (EVPs), which includes, but not limited to – exosomes and other large and small EVs, lipoproteins, exomeres/supermeres, mitochondrial‐derived vesicles, RNA binding proteins, and cell‐free DNA/RNA/proteins; (2) examining the potential functional roles and biogenesis of EVPs; (3) discussing various transcriptomic methods and technologies used in uncovering the cargoes of EVPs; (4) presenting a comprehensive list of RNA subtypes reported in EVPs; (5) describing different EV‐RNA databases and resources specific to EV‐RNA species; (6) reviewing established bioinformatics pipelines and novel strategies for reproducible EV transcriptomics analyses; (7) emphasizing the significant need for a gold standard approach in identifying EV‐RNAs across studies; (8) and finally, we highlight current challenges, discuss possible solutions, and present recommendations for robust and reproducible analyses of EVP‐associated small RNAs. Overall, we seek to provide clarity on the transcriptomics landscape, sequencing technologies, and bioinformatic analyses of EVP‐RNAs. Detailed portrayal of the current state of EVP transcriptomics will lead to a better understanding of how the RNA cargo of EVPs can be used in modern and targeted diagnostics and therapeutics. For the inclusion of different particles discussed in this article, we use the terms large/small EVs, non‐vesicular extracellular particles (NVEPs), EPs and EVPs as defined in MISEV guidelines by the International Society of Extracellular Vesicles (ISEV).

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