Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC

Lung squamous cell carcinoma (LUSC) has a poor clinical prognosis and a lack of available targeted therapies. Therefore, there is an urgent need to identify novel prognostic markers and therapeutic targets to assist in the diagnosis and treatment of LUSC. With the development of high-throughput sequ...

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Autores principales:	Jinfeng Ning, Fengjiao Wang, Kaibin Zhu, Binxi Li, Qing Shu, Wei Liu
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	copy number variation non-coding RNAs biomarkers clinical prognosis precision medicine Genetics QH426-470
Acceso en línea:	https://doaj.org/article/c1363024477341878f7b39ff89fe1d46
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spelling	oai:doaj.org-article:c1363024477341878f7b39ff89fe1d462021-12-02T00:04:13ZCharacterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC1664-802110.3389/fgene.2021.779155https://doaj.org/article/c1363024477341878f7b39ff89fe1d462021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.779155/fullhttps://doaj.org/toc/1664-8021Lung squamous cell carcinoma (LUSC) has a poor clinical prognosis and a lack of available targeted therapies. Therefore, there is an urgent need to identify novel prognostic markers and therapeutic targets to assist in the diagnosis and treatment of LUSC. With the development of high-throughput sequencing technology, integrated analysis of multi-omics data will provide annotation of pathogenic non-coding variants and the role of non-coding sequence variants in cancers. Here, we integrated RNA-seq profiles and copy number variation (CNV) data to study the effects of non-coding variations on gene regulatory network. Furthermore, the 372 long non-coding RNAs (lncRNA) regulated by CNV were used as candidate genes, which could be used as biomarkers for clinical application. Nine lncRNAs including LINC00896, MCM8-AS1, LINC01251, LNX1-AS1, GPRC5D-AS1, CTD-2350J17.1, LINC01133, LINC01121, and AC073130.1 were recognized as prognostic markers for LUSC. By exploring the association of the prognosis-related lncRNAs (pr-lncRNAs) with immune cell infiltration, GPRC5D-AS1 and LINC01133 were highlighted as markers of the immunosuppressive microenvironment. Additionally, the cascade response of pr-lncRNA-CNV-mRNA-physiological functions was revealed. Taken together, the identification of prognostic markers and carcinogenic regulatory mechanisms will contribute to the individualized treatment for LUSC and promote the development of precision medicine.Jinfeng NingFengjiao WangKaibin ZhuBinxi LiQing ShuWei LiuFrontiers Media S.A.articlecopy number variationnon-coding RNAsbiomarkersclinical prognosisprecision medicineGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	copy number variation non-coding RNAs biomarkers clinical prognosis precision medicine Genetics QH426-470
spellingShingle	copy number variation non-coding RNAs biomarkers clinical prognosis precision medicine Genetics QH426-470 Jinfeng Ning Fengjiao Wang Kaibin Zhu Binxi Li Qing Shu Wei Liu Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
description	Lung squamous cell carcinoma (LUSC) has a poor clinical prognosis and a lack of available targeted therapies. Therefore, there is an urgent need to identify novel prognostic markers and therapeutic targets to assist in the diagnosis and treatment of LUSC. With the development of high-throughput sequencing technology, integrated analysis of multi-omics data will provide annotation of pathogenic non-coding variants and the role of non-coding sequence variants in cancers. Here, we integrated RNA-seq profiles and copy number variation (CNV) data to study the effects of non-coding variations on gene regulatory network. Furthermore, the 372 long non-coding RNAs (lncRNA) regulated by CNV were used as candidate genes, which could be used as biomarkers for clinical application. Nine lncRNAs including LINC00896, MCM8-AS1, LINC01251, LNX1-AS1, GPRC5D-AS1, CTD-2350J17.1, LINC01133, LINC01121, and AC073130.1 were recognized as prognostic markers for LUSC. By exploring the association of the prognosis-related lncRNAs (pr-lncRNAs) with immune cell infiltration, GPRC5D-AS1 and LINC01133 were highlighted as markers of the immunosuppressive microenvironment. Additionally, the cascade response of pr-lncRNA-CNV-mRNA-physiological functions was revealed. Taken together, the identification of prognostic markers and carcinogenic regulatory mechanisms will contribute to the individualized treatment for LUSC and promote the development of precision medicine.
format	article
author	Jinfeng Ning Fengjiao Wang Kaibin Zhu Binxi Li Qing Shu Wei Liu
author_facet	Jinfeng Ning Fengjiao Wang Kaibin Zhu Binxi Li Qing Shu Wei Liu
author_sort	Jinfeng Ning
title	Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
title_short	Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
title_full	Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
title_fullStr	Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
title_full_unstemmed	Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC
title_sort	characterizing the copy number variation of non-coding rnas reveals potential therapeutic targets and prognostic markers of lusc
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/c1363024477341878f7b39ff89fe1d46
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_version_	1718403951213150208

Characterizing the Copy Number Variation of Non-Coding RNAs Reveals Potential Therapeutic Targets and Prognostic Markers of LUSC

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