Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations

Abstract Objectives To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four subtypes of congenital lung malformations. Methods We obtained both lesions and normal lung control t...

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Autores principales:	Weili Yang, Pu Zhao, Yun Liu, Ping Cao, Xiang Ji, Ya Gao, Peng Li, Jiwen Cheng
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Congenital lung malformations Transcriptome analysis lncRNA expression pattern Co-expression network Cis regulatory Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/5c3adbb38d154d049749e62a774ed7e5
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spelling	oai:doaj.org-article:5c3adbb38d154d049749e62a774ed7e52021-12-05T12:17:12ZTranscriptome analysis of lncRNA expression patterns in human congenital lung malformations10.1186/s12864-021-08204-x1471-2164https://doaj.org/article/5c3adbb38d154d049749e62a774ed7e52021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08204-xhttps://doaj.org/toc/1471-2164Abstract Objectives To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four subtypes of congenital lung malformations. Methods We obtained both lesions and normal lung control tissues from the patients diagnosed with CPAM-I, CPAM-II, ILS, and ILS-CPAM, and underwent lobectomy (i.e., surgical removal of the whole lobe which contains the localized lesion as well as normal lung tissue). Then, we performed lncRNA transcriptome profiling in these tissues by RNA sequencing (RNA-seq). A comprehensive bioinformatics analysis was conducted to characterize the expression profiles and relevant biological functions and for multiple comparisons of lncRNA expression in the different subtypes of congenital lung malformation tissues. Furthermore, the lncRNA-mRNA co-expression network was constructed, and dysregulated mRNAs were functionally analyzed. Finally, gene set enrichment analysis (GSEA) was used to predict the potential molecular mechanism of the identified lncRNAs. Results A total of 5921 lncRNA transcripts were identified between congenital lung malformations tissues and normal lung control tissues. Compared with normal lung control, 481of these expressed lncRNAs were upregulated and 142 were downregulated in CPAM-I, 91 were upregulated and 14 were downregulated in CPAM-II, 39 were upregulated and 38 were downregulated in ILS, and 201 were upregulated and 38 were downregulated in ILS-CPAM. Unsupervised clustering and principal component analysis of the expressed lncRNAs visualized the differences between normal lung control and different subtypes of congenital lung malformations samples. We also confirmed significant differences in the composition of differentially expressed genes (DEGs) and the differentially expressed lncRNAs (DE lncRNAs) between CPAM-I and other subtypes of congenital lung malformations, as well as in normal lung control tissues, and observed enrichment of DEGs in the regulation of the immune system, cell projection organization, and inflammatory pathways. Finally, we identified the lncRNA FLJ26850 might be related to congenital lung malformations via ZNF473. Conclusions Significant differences in lncRNAs expression patterns were observed between different subtypes of congenital lung malformations and normal control. The lncRNA FLJ26850 might be related to congenital lung malformations via ZNF473.Weili YangPu ZhaoYun LiuPing CaoXiang JiYa GaoPeng LiJiwen ChengBMCarticleCongenital lung malformationsTranscriptome analysislncRNA expression patternCo-expression networkCis regulatoryBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Congenital lung malformations Transcriptome analysis lncRNA expression pattern Co-expression network Cis regulatory Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Congenital lung malformations Transcriptome analysis lncRNA expression pattern Co-expression network Cis regulatory Biotechnology TP248.13-248.65 Genetics QH426-470 Weili Yang Pu Zhao Yun Liu Ping Cao Xiang Ji Ya Gao Peng Li Jiwen Cheng Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
description	Abstract Objectives To explore the long non-coding RNA (lncRNA) expression pattern of congenital lung malformations on a genome-wide scale and investigate their potential biological function in four subtypes of congenital lung malformations. Methods We obtained both lesions and normal lung control tissues from the patients diagnosed with CPAM-I, CPAM-II, ILS, and ILS-CPAM, and underwent lobectomy (i.e., surgical removal of the whole lobe which contains the localized lesion as well as normal lung tissue). Then, we performed lncRNA transcriptome profiling in these tissues by RNA sequencing (RNA-seq). A comprehensive bioinformatics analysis was conducted to characterize the expression profiles and relevant biological functions and for multiple comparisons of lncRNA expression in the different subtypes of congenital lung malformation tissues. Furthermore, the lncRNA-mRNA co-expression network was constructed, and dysregulated mRNAs were functionally analyzed. Finally, gene set enrichment analysis (GSEA) was used to predict the potential molecular mechanism of the identified lncRNAs. Results A total of 5921 lncRNA transcripts were identified between congenital lung malformations tissues and normal lung control tissues. Compared with normal lung control, 481of these expressed lncRNAs were upregulated and 142 were downregulated in CPAM-I, 91 were upregulated and 14 were downregulated in CPAM-II, 39 were upregulated and 38 were downregulated in ILS, and 201 were upregulated and 38 were downregulated in ILS-CPAM. Unsupervised clustering and principal component analysis of the expressed lncRNAs visualized the differences between normal lung control and different subtypes of congenital lung malformations samples. We also confirmed significant differences in the composition of differentially expressed genes (DEGs) and the differentially expressed lncRNAs (DE lncRNAs) between CPAM-I and other subtypes of congenital lung malformations, as well as in normal lung control tissues, and observed enrichment of DEGs in the regulation of the immune system, cell projection organization, and inflammatory pathways. Finally, we identified the lncRNA FLJ26850 might be related to congenital lung malformations via ZNF473. Conclusions Significant differences in lncRNAs expression patterns were observed between different subtypes of congenital lung malformations and normal control. The lncRNA FLJ26850 might be related to congenital lung malformations via ZNF473.
format	article
author	Weili Yang Pu Zhao Yun Liu Ping Cao Xiang Ji Ya Gao Peng Li Jiwen Cheng
author_facet	Weili Yang Pu Zhao Yun Liu Ping Cao Xiang Ji Ya Gao Peng Li Jiwen Cheng
author_sort	Weili Yang
title	Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
title_short	Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
title_full	Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
title_fullStr	Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
title_full_unstemmed	Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations
title_sort	transcriptome analysis of lncrna expression patterns in human congenital lung malformations
publisher	BMC
publishDate	2021
url	https://doaj.org/article/5c3adbb38d154d049749e62a774ed7e5
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_version_	1718372075235704832

Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations

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