Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations
Abstract 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, therapeu...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-12-01
|
| Series: | Journal of Extracellular Vesicles |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/jev2.70005 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841525439347032064 |
|---|---|
| author | Rebecca T. Miceli Tzu‐Yi Chen Yohei Nose Swapnil Tichkule Briana Brown John F. Fullard Marilyn D. Saulsbury Simon O. Heyliger Sacha Gnjatic Natasha Kyprianou Carlos Cordon‐Cardo Susmita Sahoo Emanuela Taioli Panos Roussos Gustavo Stolovitzky Edgar Gonzalez‐Kozlova Navneet Dogra |
| author_facet | Rebecca T. Miceli Tzu‐Yi Chen Yohei Nose Swapnil Tichkule Briana Brown John F. Fullard Marilyn D. Saulsbury Simon O. Heyliger Sacha Gnjatic Natasha Kyprianou Carlos Cordon‐Cardo Susmita Sahoo Emanuela Taioli Panos Roussos Gustavo Stolovitzky Edgar Gonzalez‐Kozlova Navneet Dogra |
| author_sort | Rebecca T. Miceli |
| collection | DOAJ |
| description | Abstract 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). |
| format | Article |
| id | doaj-art-2e84748f91d84220978959d1b1296ca7 |
| institution | Kabale University |
| issn | 2001-3078 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Extracellular Vesicles |
| spelling | doaj-art-2e84748f91d84220978959d1b1296ca72025-01-17T11:11:12ZengWileyJournal of Extracellular Vesicles2001-30782024-12-011312n/an/a10.1002/jev2.70005Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendationsRebecca T. Miceli0Tzu‐Yi Chen1Yohei Nose2Swapnil Tichkule3Briana Brown4John F. Fullard5Marilyn D. Saulsbury6Simon O. Heyliger7Sacha Gnjatic8Natasha Kyprianou9Carlos Cordon‐Cardo10Susmita Sahoo11Emanuela Taioli12Panos Roussos13Gustavo Stolovitzky14Edgar Gonzalez‐Kozlova15Navneet Dogra16Department of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of ImmunologyIcahn School of Medicine at Mount SinaiNew York New York USADepartment of Psychiatry Icahn School of Medicine at Mount Sinai New York New York USADepartment of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of Psychiatry Icahn School of Medicine at Mount Sinai New York New York USADepartment of Pharmaceutical Sciences, School of Pharmacy Hampton University Hampton Virginia USADepartment of Pharmaceutical Sciences, School of Pharmacy Hampton University Hampton Virginia USADepartment of ImmunologyIcahn School of Medicine at Mount SinaiNew York New York USADepartment of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of Medicine Icahn School of Medicine at Mount Sinai New York New York USADepartment of Population Health and Science Icahn School of Medicine at Mount Sinai New York New York USADepartment of Psychiatry Icahn School of Medicine at Mount Sinai New York New York USADepartment of Genetics and Genomics Sciences Icahn School of Medicine at Mount Sinai New York New York USADepartment of ImmunologyIcahn School of Medicine at Mount SinaiNew York New York USADepartment of Pathology, Molecular and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USAAbstract 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).https://doi.org/10.1002/jev2.70005bioinformaticsEVsextracellular vesicleslong‐read sequencingshort‐read sequencingsmall RNA |
| spellingShingle | Rebecca T. Miceli Tzu‐Yi Chen Yohei Nose Swapnil Tichkule Briana Brown John F. Fullard Marilyn D. Saulsbury Simon O. Heyliger Sacha Gnjatic Natasha Kyprianou Carlos Cordon‐Cardo Susmita Sahoo Emanuela Taioli Panos Roussos Gustavo Stolovitzky Edgar Gonzalez‐Kozlova Navneet Dogra Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations Journal of Extracellular Vesicles bioinformatics EVs extracellular vesicles long‐read sequencing short‐read sequencing small RNA |
| title | Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations |
| title_full | Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations |
| title_fullStr | Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations |
| title_full_unstemmed | Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations |
| title_short | Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations |
| title_sort | extracellular vesicles rna sequencing and bioinformatic analyses challenges solutions and recommendations |
| topic | bioinformatics EVs extracellular vesicles long‐read sequencing short‐read sequencing small RNA |
| url | https://doi.org/10.1002/jev2.70005 |
| work_keys_str_mv | AT rebeccatmiceli extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT tzuyichen extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT yoheinose extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT swapniltichkule extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT brianabrown extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT johnffullard extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT marilyndsaulsbury extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT simonoheyliger extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT sachagnjatic extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT natashakyprianou extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT carloscordoncardo extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT susmitasahoo extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT emanuelataioli extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT panosroussos extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT gustavostolovitzky extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT edgargonzalezkozlova extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations AT navneetdogra extracellularvesiclesrnasequencingandbioinformaticanalyseschallengessolutionsandrecommendations |