PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers

Ali, M.M. (Mohamad Moustafa)|||/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040; Akhade, V.S. (Vijay Suresh)|||/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628; Thankaswamy-Kosalai, S. (Subazini)|||/items/8330a760-78cc-413a-9ce1-f86f5da6888c; Subhash, S. (Santhilal)|||/items/3186ef0e-9627-463f-9da0-757cb140a4cb; Statello, L. (Luisa)|||/items/bd93ff38-fb37-46bd-9274-65da11af7f0f; Meryet-Figuiere, M. (Matthieu)|||/items/dfe0d84e-b8f5-4479-919e-78251ece22e8; Abrahamsson, J. (Jonas)|||/items/b25517f6-342c-498b-8c1b-156fc39603cb; Mondal, T. (Tanmoy)|||/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8c; Kanduri, C. (Chandrasekhar)|||/items/e10fe162-f146-47f5-a067-8335f2b99a62

PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers

Despite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncR...

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Detalles Bibliográficos
Autores:	Ali, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040, Akhade, V.S. (Vijay Suresh)\|\|\|/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628, Thankaswamy-Kosalai, S. (Subazini)\|\|\|/items/8330a760-78cc-413a-9ce1-f86f5da6888c, Subhash, S. (Santhilal)\|\|\|/items/3186ef0e-9627-463f-9da0-757cb140a4cb, Statello, L. (Luisa)\|\|\|/items/bd93ff38-fb37-46bd-9274-65da11af7f0f, Meryet-Figuiere, M. (Matthieu)\|\|\|/items/dfe0d84e-b8f5-4479-919e-78251ece22e8, Abrahamsson, J. (Jonas)\|\|\|/items/b25517f6-342c-498b-8c1b-156fc39603cb, Mondal, T. (Tanmoy)\|\|\|/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8c, Kanduri, C. (Chandrasekhar)\|\|\|/items/e10fe162-f146-47f5-a067-8335f2b99a62
Tipo de recurso:	artículo
Fecha de publicación:	2018
País:	España
Institución:	Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:	Dadun. Depósito Académico Digital de la Universidad de Navarra
Idioma:	inglés
OAI Identifier:	oai:dadun.unav.edu:10171/122273
Acceso en línea:	https://hdl.handle.net/10171/122273
Access Level:	acceso abierto
Palabra clave:	long noncoding RNAs (lncRNAs) SCAT7 patient-derived tumor (PDX) xenografts

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network_acronym_str	ES
network_name_str	España
repository_id_str
spelling	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkersAli, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040Akhade, V.S. (Vijay Suresh)\|\|\|/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628Thankaswamy-Kosalai, S. (Subazini)\|\|\|/items/8330a760-78cc-413a-9ce1-f86f5da6888cSubhash, S. (Santhilal)\|\|\|/items/3186ef0e-9627-463f-9da0-757cb140a4cbStatello, L. (Luisa)\|\|\|/items/bd93ff38-fb37-46bd-9274-65da11af7f0fMeryet-Figuiere, M. (Matthieu)\|\|\|/items/dfe0d84e-b8f5-4479-919e-78251ece22e8Abrahamsson, J. (Jonas)\|\|\|/items/b25517f6-342c-498b-8c1b-156fc39603cbMondal, T. (Tanmoy)\|\|\|/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8cKanduri, C. (Chandrasekhar)\|\|\|/items/e10fe162-f146-47f5-a067-8335f2b99a62long noncoding RNAs (lncRNAs)SCAT7patient-derived tumor (PDX) xenograftsDespite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets. Systematic clinical investigation of 14 Pan-Cancer data sets identified 633 independent prognostic markers. Silencing of the top differentially expressed and clinically relevant S-phase-enriched lncRNAs in several cancer models affects crucial cancer cell hallmarks. Mechanistic investigations on SCAT7 in multiple cancer types reveal that it interacts with hnRNPK/YBX1 complex and affects cancer cell hallmarks through the regulation of FGF/FGFR and its downstream PI3K/AKT and MAPK pathways. We also implement a LNA-antisense oligo-based strategy to treat cancer cell line and patient-derived tumor (PDX) xenografts. Thus, this study provides a comprehensive list of lncRNA-based oncogenic drivers with potential prognostic value.NatureDadun. Depósito Académico Digital Universidad de Navarra20182018-01-0120182018-01-01journal articlehttp://purl.org/coar/resource_type/c_6501info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10171/122273reponame:Dadun. Depósito Académico Digital de la Universidad de Navarrainstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:dadun.unav.edu:10171/1222732026-06-21T12:47:57Z
dc.title.none.fl_str_mv	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
title	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
spellingShingle	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers Ali, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040 long noncoding RNAs (lncRNAs) SCAT7 patient-derived tumor (PDX) xenografts
title_short	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
title_full	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
title_fullStr	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
title_full_unstemmed	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
title_sort	PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers
dc.creator.none.fl_str_mv	Ali, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040 Akhade, V.S. (Vijay Suresh)\|\|\|/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628 Thankaswamy-Kosalai, S. (Subazini)\|\|\|/items/8330a760-78cc-413a-9ce1-f86f5da6888c Subhash, S. (Santhilal)\|\|\|/items/3186ef0e-9627-463f-9da0-757cb140a4cb Statello, L. (Luisa)\|\|\|/items/bd93ff38-fb37-46bd-9274-65da11af7f0f Meryet-Figuiere, M. (Matthieu)\|\|\|/items/dfe0d84e-b8f5-4479-919e-78251ece22e8 Abrahamsson, J. (Jonas)\|\|\|/items/b25517f6-342c-498b-8c1b-156fc39603cb Mondal, T. (Tanmoy)\|\|\|/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8c Kanduri, C. (Chandrasekhar)\|\|\|/items/e10fe162-f146-47f5-a067-8335f2b99a62
author	Ali, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040
author_facet	Ali, M.M. (Mohamad Moustafa)\|\|\|/items/b992c6c3-9a2f-4b75-b4c0-c46cb5a7b040 Akhade, V.S. (Vijay Suresh)\|\|\|/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628 Thankaswamy-Kosalai, S. (Subazini)\|\|\|/items/8330a760-78cc-413a-9ce1-f86f5da6888c Subhash, S. (Santhilal)\|\|\|/items/3186ef0e-9627-463f-9da0-757cb140a4cb Statello, L. (Luisa)\|\|\|/items/bd93ff38-fb37-46bd-9274-65da11af7f0f Meryet-Figuiere, M. (Matthieu)\|\|\|/items/dfe0d84e-b8f5-4479-919e-78251ece22e8 Abrahamsson, J. (Jonas)\|\|\|/items/b25517f6-342c-498b-8c1b-156fc39603cb Mondal, T. (Tanmoy)\|\|\|/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8c Kanduri, C. (Chandrasekhar)\|\|\|/items/e10fe162-f146-47f5-a067-8335f2b99a62
author_role	author
author2	Akhade, V.S. (Vijay Suresh)\|\|\|/items/4e0f14d7-4129-4b1f-a9b3-a8cc43129628 Thankaswamy-Kosalai, S. (Subazini)\|\|\|/items/8330a760-78cc-413a-9ce1-f86f5da6888c Subhash, S. (Santhilal)\|\|\|/items/3186ef0e-9627-463f-9da0-757cb140a4cb Statello, L. (Luisa)\|\|\|/items/bd93ff38-fb37-46bd-9274-65da11af7f0f Meryet-Figuiere, M. (Matthieu)\|\|\|/items/dfe0d84e-b8f5-4479-919e-78251ece22e8 Abrahamsson, J. (Jonas)\|\|\|/items/b25517f6-342c-498b-8c1b-156fc39603cb Mondal, T. (Tanmoy)\|\|\|/items/d7593cfd-bc21-4d94-bf8a-92a1f073fa8c Kanduri, C. (Chandrasekhar)\|\|\|/items/e10fe162-f146-47f5-a067-8335f2b99a62
author2_role	author author author author author author author author
dc.contributor.none.fl_str_mv	Dadun. Depósito Académico Digital Universidad de Navarra
dc.subject.none.fl_str_mv	long noncoding RNAs (lncRNAs) SCAT7 patient-derived tumor (PDX) xenografts
topic	long noncoding RNAs (lncRNAs) SCAT7 patient-derived tumor (PDX) xenografts
description	Despite improvement in our understanding of long noncoding RNAs (lncRNAs) role in cancer, efforts to find clinically relevant cancer-associated lncRNAs are still lacking. Here, using nascent RNA capture sequencing, we identify 1145 temporally expressed S-phase-enriched lncRNAs. Among these, 570 lncRNAs show significant differential expression in at least one tumor type across TCGA data sets. Systematic clinical investigation of 14 Pan-Cancer data sets identified 633 independent prognostic markers. Silencing of the top differentially expressed and clinically relevant S-phase-enriched lncRNAs in several cancer models affects crucial cancer cell hallmarks. Mechanistic investigations on SCAT7 in multiple cancer types reveal that it interacts with hnRNPK/YBX1 complex and affects cancer cell hallmarks through the regulation of FGF/FGFR and its downstream PI3K/AKT and MAPK pathways. We also implement a LNA-antisense oligo-based strategy to treat cancer cell line and patient-derived tumor (PDX) xenografts. Thus, this study provides a comprehensive list of lncRNA-based oncogenic drivers with potential prognostic value.
publishDate	2018
dc.date.none.fl_str_mv	2018 2018-01-01 2018 2018-01-01
dc.type.none.fl_str_mv	journal article http://purl.org/coar/resource_type/c_6501
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://hdl.handle.net/10171/122273
url	https://hdl.handle.net/10171/122273
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	open access http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Nature
publisher.none.fl_str_mv	Nature
dc.source.none.fl_str_mv	reponame:Dadun. Depósito Académico Digital de la Universidad de Navarra instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str	Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str	Dadun. Depósito Académico Digital de la Universidad de Navarra
collection	Dadun. Depósito Académico Digital de la Universidad de Navarra
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score	15,198674

PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers

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