Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin, pr...

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Autores: Conrad, Thomas, Ntini, Evgenia, Lang, Benjamin, Cozzuto, Luca, Andersen, Jesper B., Marquardt, Jens U., Ponomarenko, Julia, Tartaglia, Gian Gaetano, Vang Ørom, Ulf A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/45784
Acceso en línea:http://hdl.handle.net/10230/45784
http://dx.doi.org/10.1261/rna.076240.120
Access Level:acceso abierto
Palabra clave:HCC
RNA sequencing
Clinical samples
Liver
miRNA biogenesis
Primary miRNAs
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spelling Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencingConrad, ThomasNtini, EvgeniaLang, BenjaminCozzuto, LucaAndersen, Jesper B.Marquardt, Jens U.Ponomarenko, JuliaTartaglia, Gian GaetanoVang Ørom, Ulf A.HCCRNA sequencingClinical samplesLivermiRNA biogenesisPrimary miRNAsMicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin, primary microRNAs are challenging to study in clinical samples where input material is limited. Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA that requires relatively few RNA sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma. We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease. With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.Cold Spring Harbor Laboratory Press (CSHL Press)202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/45784http://dx.doi.org/10.1261/rna.076240.120reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésRNA. 2020; 26(11):1726-30© 2020 Conrad et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.http://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/457842026-06-12T07:21:37Z
dc.title.none.fl_str_mv Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
title Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
spellingShingle Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
Conrad, Thomas
HCC
RNA sequencing
Clinical samples
Liver
miRNA biogenesis
Primary miRNAs
title_short Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
title_full Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
title_fullStr Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
title_full_unstemmed Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
title_sort Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
dc.creator.none.fl_str_mv Conrad, Thomas
Ntini, Evgenia
Lang, Benjamin
Cozzuto, Luca
Andersen, Jesper B.
Marquardt, Jens U.
Ponomarenko, Julia
Tartaglia, Gian Gaetano
Vang Ørom, Ulf A.
author Conrad, Thomas
author_facet Conrad, Thomas
Ntini, Evgenia
Lang, Benjamin
Cozzuto, Luca
Andersen, Jesper B.
Marquardt, Jens U.
Ponomarenko, Julia
Tartaglia, Gian Gaetano
Vang Ørom, Ulf A.
author_role author
author2 Ntini, Evgenia
Lang, Benjamin
Cozzuto, Luca
Andersen, Jesper B.
Marquardt, Jens U.
Ponomarenko, Julia
Tartaglia, Gian Gaetano
Vang Ørom, Ulf A.
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv HCC
RNA sequencing
Clinical samples
Liver
miRNA biogenesis
Primary miRNAs
topic HCC
RNA sequencing
Clinical samples
Liver
miRNA biogenesis
Primary miRNAs
description MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in microRNA biogenesis. Due to low expression level and association with chromatin, primary microRNAs are challenging to study in clinical samples where input material is limited. Here, we present a high-sensitivity targeted method to determine processing efficiency of several hundred primary microRNAs from total RNA that requires relatively few RNA sequencing reads. We validate the method using RNA from HeLa cells and show the applicability to clinical samples by analyzing RNA from normal liver and hepatocellular carcinoma. We identify 24 primary microRNAs with significant changes in processing efficiency from normal liver to hepatocellular carcinoma, among those the highly expressed miRNA-122 and miRNA-21, demonstrating that differential processing of primary microRNAs is occurring and could be involved in disease. With our method presented here we provide means to study pri-miRNA processing in disease from clinical samples.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
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 http://hdl.handle.net/10230/45784
http://dx.doi.org/10.1261/rna.076240.120
url http://hdl.handle.net/10230/45784
http://dx.doi.org/10.1261/rna.076240.120
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv RNA. 2020; 26(11):1726-30
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press (CSHL Press)
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press (CSHL Press)
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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