A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies

Detalhes bibliográficos
Autor(a) principal: Amorim, Maria G.
Data de Publicação: 2017
Outros Autores: 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.
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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spelling 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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