Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing
Abstract Background While numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of E...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09552-6 |
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| author | Juan-Carlos A. Padilla Seda Barutcu Ludovic Malet Gabrielle Deschamps-Francoeur Virginie Calderon Eunjeong Kwon Eric Lécuyer |
| author_facet | Juan-Carlos A. Padilla Seda Barutcu Ludovic Malet Gabrielle Deschamps-Francoeur Virginie Calderon Eunjeong Kwon Eric Lécuyer |
| author_sort | Juan-Carlos A. Padilla |
| collection | DOAJ |
| description | Abstract Background While numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-targeted RNA populations. It has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and the extent to which full-length mRNAs are present within EVs remains to be clarified. Results Using long-read nanopore RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 443 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 10.58% of all EV reads, and 18.67% of all cellular (WC) reads, corresponded to known full-length transcripts, with mRNAs representing the largest biotype for each group (EV = 58.13%, WC = 43.93%). We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. Conclusion This work provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs, while also underscoring the potential usefulness of nanopore sequencing to interrogate secreted RNA transcriptomes. |
| first_indexed | 2024-03-10T22:15:29Z |
| format | Article |
| id | doaj.art-80420b5be2794aa5b62fa8cda0442f39 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-10T22:15:29Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-80420b5be2794aa5b62fa8cda0442f392023-11-19T12:27:50ZengBMCBMC Genomics1471-21642023-09-0124111610.1186/s12864-023-09552-6Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencingJuan-Carlos A. Padilla0Seda Barutcu1Ludovic Malet2Gabrielle Deschamps-Francoeur3Virginie Calderon4Eunjeong Kwon5Eric Lécuyer6Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Institut de Recherches Cliniques de Montréal (IRCM)Abstract Background While numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-targeted RNA populations. It has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and the extent to which full-length mRNAs are present within EVs remains to be clarified. Results Using long-read nanopore RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 443 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 10.58% of all EV reads, and 18.67% of all cellular (WC) reads, corresponded to known full-length transcripts, with mRNAs representing the largest biotype for each group (EV = 58.13%, WC = 43.93%). We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. Conclusion This work provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs, while also underscoring the potential usefulness of nanopore sequencing to interrogate secreted RNA transcriptomes.https://doi.org/10.1186/s12864-023-09552-6Extracellular vesiclesLong-Read RNA SequencingNanopore sequencingPolyadenylated transcriptomePoly-AmRNA |
| spellingShingle | Juan-Carlos A. Padilla Seda Barutcu Ludovic Malet Gabrielle Deschamps-Francoeur Virginie Calderon Eunjeong Kwon Eric Lécuyer Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing BMC Genomics Extracellular vesicles Long-Read RNA Sequencing Nanopore sequencing Polyadenylated transcriptome Poly-A mRNA |
| title | Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing |
| title_full | Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing |
| title_fullStr | Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing |
| title_full_unstemmed | Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing |
| title_short | Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing |
| title_sort | profiling the polyadenylated transcriptome of extracellular vesicles with long read nanopore sequencing |
| topic | Extracellular vesicles Long-Read RNA Sequencing Nanopore sequencing Polyadenylated transcriptome Poly-A mRNA |
| url | https://doi.org/10.1186/s12864-023-09552-6 |
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