Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles

Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencin...

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Autores: Solaguren Beascoa, Maria, Gámez Valero, Ana, Escaramís Babiano, Geòrgia, Herrero Lorenzo, Marina, Ortiz, Ana M., Minguet, Carla, Gonzalo, Ricardo, Bravo, Maria Isabel, Costa, Montserrat, Martí, Eulàlia
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Recursos:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/218797
Acesso em linha:https://hdl.handle.net/2445/218797
Access Level:acceso abierto
Palavra-chave:Marcadors bioquímics
RNA
Micro RNAs
Genètica
Biochemical markers
MicroRNAs
Genetics
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spelling Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesiclesSolaguren Beascoa, MariaGámez Valero, AnaEscaramís Babiano, GeòrgiaHerrero Lorenzo, MarinaOrtiz, Ana M.Minguet, CarlaGonzalo, RicardoBravo, Maria IsabelCosta, MontserratMartí, EulàliaMarcadors bioquímicsRNAMicro RNAsGenèticaBiochemical markersRNAMicroRNAsGeneticsSmall RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.MDPI2023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/218797Articles publicats en revistes (Biomedicina)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.3390/ijms241411653International Journal of Molecular Sciences, 2023, vol. 24, num.14https://doi.org/10.3390/ijms241411653cc-by (c) Solaguren-Beascoa, M. et al., 2023http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2187972026-05-27T06:46:51Z
dc.title.none.fl_str_mv Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
title Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
spellingShingle Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
Solaguren Beascoa, Maria
Marcadors bioquímics
RNA
Micro RNAs
Genètica
Biochemical markers
RNA
MicroRNAs
Genetics
title_short Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
title_full Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
title_fullStr Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
title_full_unstemmed Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
title_sort Phospho-RNA-Seq highlights specific small RNA profiles in plasma extracellular vesicles
dc.creator.none.fl_str_mv Solaguren Beascoa, Maria
Gámez Valero, Ana
Escaramís Babiano, Geòrgia
Herrero Lorenzo, Marina
Ortiz, Ana M.
Minguet, Carla
Gonzalo, Ricardo
Bravo, Maria Isabel
Costa, Montserrat
Martí, Eulàlia
author Solaguren Beascoa, Maria
author_facet Solaguren Beascoa, Maria
Gámez Valero, Ana
Escaramís Babiano, Geòrgia
Herrero Lorenzo, Marina
Ortiz, Ana M.
Minguet, Carla
Gonzalo, Ricardo
Bravo, Maria Isabel
Costa, Montserrat
Martí, Eulàlia
author_role author
author2 Gámez Valero, Ana
Escaramís Babiano, Geòrgia
Herrero Lorenzo, Marina
Ortiz, Ana M.
Minguet, Carla
Gonzalo, Ricardo
Bravo, Maria Isabel
Costa, Montserrat
Martí, Eulàlia
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Marcadors bioquímics
RNA
Micro RNAs
Genètica
Biochemical markers
RNA
MicroRNAs
Genetics
topic Marcadors bioquímics
RNA
Micro RNAs
Genètica
Biochemical markers
RNA
MicroRNAs
Genetics
description Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/218797
url https://hdl.handle.net/2445/218797
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.3390/ijms241411653
International Journal of Molecular Sciences, 2023, vol. 24, num.14
https://doi.org/10.3390/ijms241411653
dc.rights.none.fl_str_mv cc-by (c) Solaguren-Beascoa, M. et al., 2023
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Solaguren-Beascoa, M. et al., 2023
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv Articles publicats en revistes (Biomedicina)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.81155

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