Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC
Abstract Background Extracellular vesicles (EVs) from human umbilical cord mesenchymal stem cells (hUMSCs) are widely considered to be the best mediators for cell-free therapy. An understanding of their composition, especially RNA, is particularly important for the safe and precise application of EV...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | Stem Cell Research & Therapy |
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| Online Access: | https://doi.org/10.1186/s13287-023-03491-5 |
| _version_ | 1797577736257011712 |
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| author | Dong Yu Yue Mei Ling Wang Yunpeng Zhao Xingfei Fan Dong Liang Li Li Jie Zhu Sisi Bi Xue Wang Zhongquan Qi Lie Zhu Yue Wang |
| author_facet | Dong Yu Yue Mei Ling Wang Yunpeng Zhao Xingfei Fan Dong Liang Li Li Jie Zhu Sisi Bi Xue Wang Zhongquan Qi Lie Zhu Yue Wang |
| author_sort | Dong Yu |
| collection | DOAJ |
| description | Abstract Background Extracellular vesicles (EVs) from human umbilical cord mesenchymal stem cells (hUMSCs) are widely considered to be the best mediators for cell-free therapy. An understanding of their composition, especially RNA, is particularly important for the safe and precise application of EVs. Up to date, the knowledge of their RNA components is limited to NGS sequencing and cannot provide a comprehensive transcriptomic landscape, especially the long and full-length transcripts. Our study first focused on the transcriptomic profile of hUMSC-EVs based on nanopore sequencing. Methods In this study, different EV subtypes (exosomes and microvesicles) derived from hUMSCs were isolated and identified by density gradient centrifugation. Subsequently, the realistic long transcriptomic profile in different subtypes of hUMSC-EVs was systematically compared by nanopore sequencing and bioinformatic analysis. Results Abundant transcript variants were identified in EVs by nanopore sequencing, 69.34% of which transcripts were fragmented. A series of full-length and long transcripts was also observed and showed a significantly higher proportion of intact or near-complete transcripts in exosomes than that in microvesicles derived from hUMSCs. Although the composition of RNA biotypes transported by different EV subtypes was similar, the distribution of transcripts and genes revealed the inter-heterogeneity and intra-stability between exosomes and microvesicles. Further, 85 different expressed transcripts (56 genes) and 7 fusion genes were identified. Pathway enrichment analysis showed that upregulated-expressed genes in microvesicles were mainly enriched in multiple neurodegenerative diseases, while upregulated-expressed genes in exosomes were mainly enriched in neutrophil extracellular trap formation, suggesting different functional tendencies of EV subtypes. Conclusions This study provides a novel understanding of different types of hUMSC-EVs, which not only suggests different transcriptome sorting mechanisms between exosomes and microvesicles, but also shows that different EV subtypes from the same source have different physiological functions, suggesting distinct clinical application prospects. |
| first_indexed | 2024-03-10T22:12:14Z |
| format | Article |
| id | doaj.art-47350a1c78174f898d7afd3a3432eb9f |
| institution | Directory Open Access Journal |
| issn | 1757-6512 |
| language | English |
| last_indexed | 2024-03-10T22:12:14Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Stem Cell Research & Therapy |
| spelling | doaj.art-47350a1c78174f898d7afd3a3432eb9f2023-11-19T12:33:25ZengBMCStem Cell Research & Therapy1757-65122023-09-0114111310.1186/s13287-023-03491-5Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSCDong Yu0Yue Mei1Ling Wang2Yunpeng Zhao3Xingfei Fan4Dong Liang5Li Li6Jie Zhu7Sisi Bi8Xue Wang9Zhongquan Qi10Lie Zhu11Yue Wang12Department of Precision Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Precision Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Precision Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Precision Medicine, Translational Medicine Research Center, Naval Medical UniversityDepartment of Histology and Embryology, Basic Medicine Collage, Naval Medical UniversityDepartment of Plastic and Reconstructive Surgery, Secondary Affiliated Hospital of Naval Medical UniversityMedical College of Guangxi UniversityMedical College of Guangxi UniversityMedical College of Guangxi UniversityDepartment of Plastic and Reconstructive Surgery, Secondary Affiliated Hospital of Naval Medical UniversityDepartment of Stem Cell and Regeneration Medicine, Translational Medicine Research Center, Naval Medical UniversityAbstract Background Extracellular vesicles (EVs) from human umbilical cord mesenchymal stem cells (hUMSCs) are widely considered to be the best mediators for cell-free therapy. An understanding of their composition, especially RNA, is particularly important for the safe and precise application of EVs. Up to date, the knowledge of their RNA components is limited to NGS sequencing and cannot provide a comprehensive transcriptomic landscape, especially the long and full-length transcripts. Our study first focused on the transcriptomic profile of hUMSC-EVs based on nanopore sequencing. Methods In this study, different EV subtypes (exosomes and microvesicles) derived from hUMSCs were isolated and identified by density gradient centrifugation. Subsequently, the realistic long transcriptomic profile in different subtypes of hUMSC-EVs was systematically compared by nanopore sequencing and bioinformatic analysis. Results Abundant transcript variants were identified in EVs by nanopore sequencing, 69.34% of which transcripts were fragmented. A series of full-length and long transcripts was also observed and showed a significantly higher proportion of intact or near-complete transcripts in exosomes than that in microvesicles derived from hUMSCs. Although the composition of RNA biotypes transported by different EV subtypes was similar, the distribution of transcripts and genes revealed the inter-heterogeneity and intra-stability between exosomes and microvesicles. Further, 85 different expressed transcripts (56 genes) and 7 fusion genes were identified. Pathway enrichment analysis showed that upregulated-expressed genes in microvesicles were mainly enriched in multiple neurodegenerative diseases, while upregulated-expressed genes in exosomes were mainly enriched in neutrophil extracellular trap formation, suggesting different functional tendencies of EV subtypes. Conclusions This study provides a novel understanding of different types of hUMSC-EVs, which not only suggests different transcriptome sorting mechanisms between exosomes and microvesicles, but also shows that different EV subtypes from the same source have different physiological functions, suggesting distinct clinical application prospects.https://doi.org/10.1186/s13287-023-03491-5Extracellular vesicles subtypesNanopore sequencingTranscriptomic landscape |
| spellingShingle | Dong Yu Yue Mei Ling Wang Yunpeng Zhao Xingfei Fan Dong Liang Li Li Jie Zhu Sisi Bi Xue Wang Zhongquan Qi Lie Zhu Yue Wang Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC Stem Cell Research & Therapy Extracellular vesicles subtypes Nanopore sequencing Transcriptomic landscape |
| title | Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC |
| title_full | Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC |
| title_fullStr | Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC |
| title_full_unstemmed | Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC |
| title_short | Nano-seq analysis reveals different functional tendency between exosomes and microvesicles derived from hUMSC |
| title_sort | nano seq analysis reveals different functional tendency between exosomes and microvesicles derived from humsc |
| topic | Extracellular vesicles subtypes Nanopore sequencing Transcriptomic landscape |
| url | https://doi.org/10.1186/s13287-023-03491-5 |
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