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Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles

SIMPLE SUMMARY: Small RNA sequencing has been widely used for characterizing the landscape of small non-coding RNAs—the most abundant cargo in extracellular vesicles (EVs). Here, we performed a systematic assessment of the quality, technical, and potential biological biases introduced by different E...

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Autores principales: Wang, Jing, Chen, Hua-Chang, Sheng, Quanhu, Dawson, T. Renee, Coffey, Robert J., Patton, James G., Weaver, Alissa M., Shyr, Yu, Liu, Qi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10340377/
https://www.ncbi.nlm.nih.gov/pubmed/37444556
http://dx.doi.org/10.3390/cancers15133446
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author Wang, Jing
Chen, Hua-Chang
Sheng, Quanhu
Dawson, T. Renee
Coffey, Robert J.
Patton, James G.
Weaver, Alissa M.
Shyr, Yu
Liu, Qi
author_facet Wang, Jing
Chen, Hua-Chang
Sheng, Quanhu
Dawson, T. Renee
Coffey, Robert J.
Patton, James G.
Weaver, Alissa M.
Shyr, Yu
Liu, Qi
author_sort Wang, Jing
collection PubMed
description SIMPLE SUMMARY: Small RNA sequencing has been widely used for characterizing the landscape of small non-coding RNAs—the most abundant cargo in extracellular vesicles (EVs). Here, we performed a systematic assessment of the quality, technical, and potential biological biases introduced by different EV isolation methods and the enrichment of specific, small RNA biotypes in EVs. The findings in this study guide the quality control of EV small RNA-seq and the selection of EV isolation techniques and enhance the interpretation of small RNA contents and the preferential loading of specific RNA biotypes into EVs. ABSTRACT: Motivation: Extracellular vesicles (EVs) are produced and released by most cells and are now recognized to play a role in intercellular communication through the delivery of molecular cargo, including proteins, lipids, and RNA. Small RNA sequencing (small RNA-seq) has been widely used to characterize the small RNA content in EVs. However, there is a lack of a systematic assessment of the quality, technical biases, RNA composition, and RNA biotypes enrichment for small RNA profiling of EVs across cell types, biofluids, and conditions. Methods: We collected and reanalyzed small RNA-seq datasets for 2756 samples from 83 studies involving 55 with EVs only and 28 with both EVs and matched donor cells. We assessed their quality by the total number of reads after adapter trimming, the overall alignment rate to the host and non-host genomes, and the proportional abundance of total small RNA and specific biotypes, such as miRNA, tRNA, rRNA, and Y RNA. Results: We found that EV extraction methods varied in their reproducibility in isolating small RNAs, with effects on small RNA composition. Comparing proportional abundances of RNA biotypes between EVs and matched donor cells, we discovered that rRNA and tRNA fragments were relatively enriched, but miRNAs and snoRNA were depleted in EVs. Except for the export of eight miRNAs being context-independent, the selective release of most miRNAs into EVs was study-specific. Conclusion: This work guides quality control and the selection of EV isolation methods and enhances the interpretation of small RNA contents and preferential loading in EVs.
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spelling pubmed-103403772023-07-14 Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles Wang, Jing Chen, Hua-Chang Sheng, Quanhu Dawson, T. Renee Coffey, Robert J. Patton, James G. Weaver, Alissa M. Shyr, Yu Liu, Qi Cancers (Basel) Article SIMPLE SUMMARY: Small RNA sequencing has been widely used for characterizing the landscape of small non-coding RNAs—the most abundant cargo in extracellular vesicles (EVs). Here, we performed a systematic assessment of the quality, technical, and potential biological biases introduced by different EV isolation methods and the enrichment of specific, small RNA biotypes in EVs. The findings in this study guide the quality control of EV small RNA-seq and the selection of EV isolation techniques and enhance the interpretation of small RNA contents and the preferential loading of specific RNA biotypes into EVs. ABSTRACT: Motivation: Extracellular vesicles (EVs) are produced and released by most cells and are now recognized to play a role in intercellular communication through the delivery of molecular cargo, including proteins, lipids, and RNA. Small RNA sequencing (small RNA-seq) has been widely used to characterize the small RNA content in EVs. However, there is a lack of a systematic assessment of the quality, technical biases, RNA composition, and RNA biotypes enrichment for small RNA profiling of EVs across cell types, biofluids, and conditions. Methods: We collected and reanalyzed small RNA-seq datasets for 2756 samples from 83 studies involving 55 with EVs only and 28 with both EVs and matched donor cells. We assessed their quality by the total number of reads after adapter trimming, the overall alignment rate to the host and non-host genomes, and the proportional abundance of total small RNA and specific biotypes, such as miRNA, tRNA, rRNA, and Y RNA. Results: We found that EV extraction methods varied in their reproducibility in isolating small RNAs, with effects on small RNA composition. Comparing proportional abundances of RNA biotypes between EVs and matched donor cells, we discovered that rRNA and tRNA fragments were relatively enriched, but miRNAs and snoRNA were depleted in EVs. Except for the export of eight miRNAs being context-independent, the selective release of most miRNAs into EVs was study-specific. Conclusion: This work guides quality control and the selection of EV isolation methods and enhances the interpretation of small RNA contents and preferential loading in EVs. MDPI 2023-06-30 /pmc/articles/PMC10340377/ /pubmed/37444556 http://dx.doi.org/10.3390/cancers15133446 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Jing
Chen, Hua-Chang
Sheng, Quanhu
Dawson, T. Renee
Coffey, Robert J.
Patton, James G.
Weaver, Alissa M.
Shyr, Yu
Liu, Qi
Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title_full Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title_fullStr Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title_full_unstemmed Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title_short Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
title_sort systematic assessment of small rna profiling in human extracellular vesicles
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10340377/
https://www.ncbi.nlm.nih.gov/pubmed/37444556
http://dx.doi.org/10.3390/cancers15133446
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