A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | http://dx.doi.org/10.1038/s41598-017-14264-5 https://repositorio.unifesp.br/handle/11600/57128 |
Resumo: | Extracellular vesicles (EVs) are key mediators of intercellular communication. Part of their biological effects can be attributed to the transfer of cargos of diverse types of RNAs, which are promising diagnostic and prognostic biomarkers. EVs found in human biofluids are a valuable source for the development of minimally invasive assays. However, the total transcriptional landscape of EVs is still largely unknown. Here we develop a new method for total transcriptome profiling of plasma-derived EVs by next generation sequencing (NGS) from limited quantities of patient-derived clinical samples, which enables the unbiased characterization of the complete RNA cargo, including both small- and long-RNAs, in a single library preparation step. This approach was applied to RNA extracted from EVs isolated by ultracentrifugation from the plasma of five healthy volunteers. Among the most abundant RNAs identified we found small RNAs such as tRNAs, miRNAs and miscellaneous RNAs, which have largely unknown functions. We also identified protein-coding and long noncoding transcripts, as well as circular RNA species that were also experimentally validated. This method enables, for the first time, the full spectrum of transcriptome data to be obtained from minute patient-derived samples, and will therefore potentially allow the identification of cell-to-cell communication mechanisms and biomarkers. |
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A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsiesExtracellular vesicles (EVs) are key mediators of intercellular communication. Part of their biological effects can be attributed to the transfer of cargos of diverse types of RNAs, which are promising diagnostic and prognostic biomarkers. EVs found in human biofluids are a valuable source for the development of minimally invasive assays. However, the total transcriptional landscape of EVs is still largely unknown. Here we develop a new method for total transcriptome profiling of plasma-derived EVs by next generation sequencing (NGS) from limited quantities of patient-derived clinical samples, which enables the unbiased characterization of the complete RNA cargo, including both small- and long-RNAs, in a single library preparation step. This approach was applied to RNA extracted from EVs isolated by ultracentrifugation from the plasma of five healthy volunteers. Among the most abundant RNAs identified we found small RNAs such as tRNAs, miRNAs and miscellaneous RNAs, which have largely unknown functions. We also identified protein-coding and long noncoding transcripts, as well as circular RNA species that were also experimentally validated. This method enables, for the first time, the full spectrum of transcriptome data to be obtained from minute patient-derived samples, and will therefore potentially allow the identification of cell-to-cell communication mechanisms and biomarkers.AC Camargo Canc Ctr, Lab Med Genom, Sao Paulo, SP, BrazilAC Camargo Canc Ctr, Lab Computat Biol, Sao Paulo, SP, BrazilUniv Sao Paulo, Inst Biomed Sci, Dept Cell & Dev Biol, Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Electron Microscopy Ctr, Sao Paulo, SP, BrazilUniv Texas MD Anderson Canc Ctr, Dept Expt Therapeut, Houston, TX 77030 USAUniv Texas MD Anderson Canc Ctr, Ctr RNA Interference & Non Coding RNAs, Houston, TX 77030 USAUniv New Mexico, Comprehens Canc Ctr, Albuquerque, NM 87131 USAUniv New Mexico, Sch Med, Div Hematol Oncol, Dept Internal Med, Albuquerque, NM 87131 USAUniv New Mexico, Sch Med, Div Mol Med, Dept Internal Med, Albuquerque, NM 87131 USARockefeller Univ, Lab Mol Immunol, 1230 York Ave, New York, NY 10021 USAFMUSP, Lab Neurociencias Alzira Denise Hertzog Silva LIM, Inst Psiquiatria, Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Electron Microscopy Ctr, Sao Paulo, SP, BrazilWeb of ScienceFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Gillson-Longenbaugh FoundationNational Institutes of Health (NIH/NCATS) through the NIH Common Fund, Office of Strategic Coordination (OSC)FAPESP: 2011/09172-3FAPESP: 2014/26897-0Nature Publishing Group2020-08-04T13:39:48Z2020-08-04T13:39:48Z2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersion-application/pdfhttp://dx.doi.org/10.1038/s41598-017-14264-5Scientific Reports. London, v. 7, p. -, 2017.10.1038/s41598-017-14264-5WOS000414230900006.pdf2045-2322https://repositorio.unifesp.br/handle/11600/57128WOS:000414230900006engScientific ReportsLondoninfo:eu-repo/semantics/openAccessAmorim, Maria G.Valieris, RenanDrummond, Rodrigo D.Pizzi, Melissa P.Freitas, Vanessa M.Sinigaglia-Coimbra, Rita [UNIFESP]Calin, George A.Pasqualini, RenataArap, WadihSilva, Israel T.Dias-Neto, EmmanuelNunes, Diana N.reponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESP2024-07-27T20:00:50Zoai:repositorio.unifesp.br/:11600/57128Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestbiblioteca.csp@unifesp.bropendoar:34652024-07-27T20:00:50Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.none.fl_str_mv |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
title |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
spellingShingle |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies Amorim, Maria G. |
title_short |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
title_full |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
title_fullStr |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
title_full_unstemmed |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
title_sort |
A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies |
author |
Amorim, Maria G. |
author_facet |
Amorim, Maria G. Valieris, Renan Drummond, Rodrigo D. Pizzi, Melissa P. Freitas, Vanessa M. Sinigaglia-Coimbra, Rita [UNIFESP] Calin, George A. Pasqualini, Renata Arap, Wadih Silva, Israel T. Dias-Neto, Emmanuel Nunes, Diana N. |
author_role |
author |
author2 |
Valieris, Renan Drummond, Rodrigo D. Pizzi, Melissa P. Freitas, Vanessa M. Sinigaglia-Coimbra, Rita [UNIFESP] Calin, George A. Pasqualini, Renata Arap, Wadih Silva, Israel T. Dias-Neto, Emmanuel Nunes, Diana N. |
author2_role |
author author author author author author author author author author author |
dc.contributor.author.fl_str_mv |
Amorim, Maria G. Valieris, Renan Drummond, Rodrigo D. Pizzi, Melissa P. Freitas, Vanessa M. Sinigaglia-Coimbra, Rita [UNIFESP] Calin, George A. Pasqualini, Renata Arap, Wadih Silva, Israel T. Dias-Neto, Emmanuel Nunes, Diana N. |
description |
Extracellular vesicles (EVs) are key mediators of intercellular communication. Part of their biological effects can be attributed to the transfer of cargos of diverse types of RNAs, which are promising diagnostic and prognostic biomarkers. EVs found in human biofluids are a valuable source for the development of minimally invasive assays. However, the total transcriptional landscape of EVs is still largely unknown. Here we develop a new method for total transcriptome profiling of plasma-derived EVs by next generation sequencing (NGS) from limited quantities of patient-derived clinical samples, which enables the unbiased characterization of the complete RNA cargo, including both small- and long-RNAs, in a single library preparation step. This approach was applied to RNA extracted from EVs isolated by ultracentrifugation from the plasma of five healthy volunteers. Among the most abundant RNAs identified we found small RNAs such as tRNAs, miRNAs and miscellaneous RNAs, which have largely unknown functions. We also identified protein-coding and long noncoding transcripts, as well as circular RNA species that were also experimentally validated. This method enables, for the first time, the full spectrum of transcriptome data to be obtained from minute patient-derived samples, and will therefore potentially allow the identification of cell-to-cell communication mechanisms and biomarkers. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017 2020-08-04T13:39:48Z 2020-08-04T13:39:48Z |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1038/s41598-017-14264-5 Scientific Reports. London, v. 7, p. -, 2017. 10.1038/s41598-017-14264-5 WOS000414230900006.pdf 2045-2322 https://repositorio.unifesp.br/handle/11600/57128 WOS:000414230900006 |
url |
http://dx.doi.org/10.1038/s41598-017-14264-5 https://repositorio.unifesp.br/handle/11600/57128 |
identifier_str_mv |
Scientific Reports. London, v. 7, p. -, 2017. 10.1038/s41598-017-14264-5 WOS000414230900006.pdf 2045-2322 WOS:000414230900006 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Scientific Reports |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
- application/pdf |
dc.coverage.none.fl_str_mv |
London |
dc.publisher.none.fl_str_mv |
Nature Publishing Group |
publisher.none.fl_str_mv |
Nature Publishing Group |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UNIFESP instname:Universidade Federal de São Paulo (UNIFESP) instacron:UNIFESP |
instname_str |
Universidade Federal de São Paulo (UNIFESP) |
instacron_str |
UNIFESP |
institution |
UNIFESP |
reponame_str |
Repositório Institucional da UNIFESP |
collection |
Repositório Institucional da UNIFESP |
repository.name.fl_str_mv |
Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP) |
repository.mail.fl_str_mv |
biblioteca.csp@unifesp.br |
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1814268310890479616 |