Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles
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 characteriz...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/15/13/3446 |
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| author | Jing Wang Hua-Chang Chen Quanhu Sheng T. Renee Dawson Robert J. Coffey James G. Patton Alissa M. Weaver Yu Shyr Qi Liu |
| author_facet | Jing Wang Hua-Chang Chen Quanhu Sheng T. Renee Dawson Robert J. Coffey James G. Patton Alissa M. Weaver Yu Shyr Qi Liu |
| author_sort | Jing Wang |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T01:44:50Z |
| format | Article |
| id | doaj.art-1815acaae4ec411aa6ae7a282a189d62 |
| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-11T01:44:50Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-1815acaae4ec411aa6ae7a282a189d622023-11-18T16:17:07ZengMDPI AGCancers2072-66942023-06-011513344610.3390/cancers15133446Systematic Assessment of Small RNA Profiling in Human Extracellular VesiclesJing Wang0Hua-Chang Chen1Quanhu Sheng2T. Renee Dawson3Robert J. Coffey4James G. Patton5Alissa M. Weaver6Yu Shyr7Qi Liu8Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USADepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USADepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USADepartment of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USADepartment of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USADepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USADepartment of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USADepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USADepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USAMotivation: 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.https://www.mdpi.com/2072-6694/15/13/3446extracellular vesiclessmall RNA-seqquality controltechnical biasesRNA compositionRNA biotypes enrichment |
| spellingShingle | Jing Wang Hua-Chang Chen Quanhu Sheng T. Renee Dawson Robert J. Coffey James G. Patton Alissa M. Weaver Yu Shyr Qi Liu Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles Cancers extracellular vesicles small RNA-seq quality control technical biases RNA composition RNA biotypes enrichment |
| 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 | extracellular vesicles small RNA-seq quality control technical biases RNA composition RNA biotypes enrichment |
| url | https://www.mdpi.com/2072-6694/15/13/3446 |
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