Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples

Simple Summary Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer pat...

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Autores: Iraola-Guzman, S, Brunet-Vega, A, Pegueroles, C, Saus, E, Hovhannisyan, H, Casalots, A, Pericay, C, Gabaldon, T
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Recursos:Institut d'Investigació i Innovació Parc Taulí (I3PT)
Repositorio:r-I3PT. Repositorio Institucional Producción Científica del Institut d'Investigació i Innovació Parc Taulí
OAI Identifier:oai:i3pt.fundanetsuite.com:p2462
Acesso em linha:https://i3pt.portalinvestigacion.com/publicaciones/2462
Access Level:acceso abierto
Palavra-chave:lncRNAs enrichment
CRC
FFPE samples
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spelling Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer SamplesIraola-Guzman, SBrunet-Vega, APegueroles, CSaus, EHovhannisyan, HCasalots, APericay, CGabaldon, TlncRNAs enrichmentCRCFFPE samplesSimple Summary Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer patients is challenging, and new biomarkers are required to identify patients with high probability of relapse. We focused on translational potential of non-coding RNAs in colorectal cancer. In this study, we aim to validate a new tool which couples target enrichment and RNAseq for transcriptomics studies of lncRNAs in formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that this new approach efficiently detects lncRNAs and differences in their expression between healthy and tumor FFPE tissues, as well as somatic mutations in expressed lncRNAs, identifying novel lncRNAs as potential candidates for colorectal cancer. This new approach could represent a promising avenue that would reduce costs and enable more efficient translational research. Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.MDPI2020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://i3pt.portalinvestigacion.com/publicaciones/2462CancersISSN: 20726694reponame:r-I3PT. Repositorio Institucional Producción Científica del Institut d'Investigació i Innovació Parc Taulíinstname:Institut d'Investigació i Innovació Parc Taulí (I3PT)Inglésinfo:eu-repo/semantics/openAccessoai:i3pt.fundanetsuite.com:p24622026-06-21T15:30:37Z
dc.title.none.fl_str_mv Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
title Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
spellingShingle Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
Iraola-Guzman, S
lncRNAs enrichment
CRC
FFPE samples
title_short Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
title_full Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
title_fullStr Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
title_full_unstemmed Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
title_sort Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
dc.creator.none.fl_str_mv Iraola-Guzman, S
Brunet-Vega, A
Pegueroles, C
Saus, E
Hovhannisyan, H
Casalots, A
Pericay, C
Gabaldon, T
author Iraola-Guzman, S
author_facet Iraola-Guzman, S
Brunet-Vega, A
Pegueroles, C
Saus, E
Hovhannisyan, H
Casalots, A
Pericay, C
Gabaldon, T
author_role author
author2 Brunet-Vega, A
Pegueroles, C
Saus, E
Hovhannisyan, H
Casalots, A
Pericay, C
Gabaldon, T
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv lncRNAs enrichment
CRC
FFPE samples
topic lncRNAs enrichment
CRC
FFPE samples
description Simple Summary Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer patients is challenging, and new biomarkers are required to identify patients with high probability of relapse. We focused on translational potential of non-coding RNAs in colorectal cancer. In this study, we aim to validate a new tool which couples target enrichment and RNAseq for transcriptomics studies of lncRNAs in formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that this new approach efficiently detects lncRNAs and differences in their expression between healthy and tumor FFPE tissues, as well as somatic mutations in expressed lncRNAs, identifying novel lncRNAs as potential candidates for colorectal cancer. This new approach could represent a promising avenue that would reduce costs and enable more efficient translational research. Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.
publishDate 2020
dc.date.none.fl_str_mv 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 https://i3pt.portalinvestigacion.com/publicaciones/2462
url https://i3pt.portalinvestigacion.com/publicaciones/2462
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv Cancers
ISSN: 20726694
reponame:r-I3PT. Repositorio Institucional Producción Científica del Institut d'Investigació i Innovació Parc Taulí
instname:Institut d'Investigació i Innovació Parc Taulí (I3PT)
instname_str Institut d'Investigació i Innovació Parc Taulí (I3PT)
reponame_str r-I3PT. Repositorio Institucional Producción Científica del Institut d'Investigació i Innovació Parc Taulí
collection r-I3PT. Repositorio Institucional Producción Científica del Institut d'Investigació i Innovació Parc Taulí
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812455

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