Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma

Abstract Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relation...

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Autores principales:	Priyanka Banerjee, Premanand Balraj, Nilesh Sudhakar Ambhore, Sarah A. Wicher, Rodney D. Britt, Christina M. Pabelick, Y. S. Prakash, Venkatachalem Sathish
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8b34563885034ee5adaba98fb6aef59d
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spelling	oai:doaj.org-article:8b34563885034ee5adaba98fb6aef59d2021-12-02T16:14:03ZNetwork and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma10.1038/s41598-021-93845-x2045-2322https://doaj.org/article/8b34563885034ee5adaba98fb6aef59d2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93845-xhttps://doaj.org/toc/2045-2322Abstract Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relationship between ASM genes to uncover the putative mechanism underlying asthma in humans. To this end, the gene expression from human ASM was measured with RNA-Seq in non-asthmatic and asthmatic groups. The gene network for the asthmatic and non-asthmatic group was constructed by prioritizing differentially expressed genes (DEGs) (121) and transcription factors (TFs) (116). Furthermore, we identified differentially connected or co-expressed genes in each group. The asthmatic group showed a loss of gene connectivity due to the rewiring of major regulators. Notably, TFs such as ZNF792, SMAD1, and SMAD7 were differentially correlated in the asthmatic ASM. Additionally, the DEGs, TFs, and differentially connected genes over-represented in the pathways involved with herpes simplex virus infection, Hippo and TGF-β signaling, adherens junctions, gap junctions, and ferroptosis. The rewiring of major regulators unveiled in this study likely modulates the expression of gene-targets as an adaptive response to asthma. These multiple gene interactions pointed out novel targets and pathways for asthma exacerbations.Priyanka BanerjeePremanand BalrajNilesh Sudhakar AmbhoreSarah A. WicherRodney D. BrittChristina M. PabelickY. S. PrakashVenkatachalem SathishNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Priyanka Banerjee Premanand Balraj Nilesh Sudhakar Ambhore Sarah A. Wicher Rodney D. Britt Christina M. Pabelick Y. S. Prakash Venkatachalem Sathish Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
description	Abstract Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relationship between ASM genes to uncover the putative mechanism underlying asthma in humans. To this end, the gene expression from human ASM was measured with RNA-Seq in non-asthmatic and asthmatic groups. The gene network for the asthmatic and non-asthmatic group was constructed by prioritizing differentially expressed genes (DEGs) (121) and transcription factors (TFs) (116). Furthermore, we identified differentially connected or co-expressed genes in each group. The asthmatic group showed a loss of gene connectivity due to the rewiring of major regulators. Notably, TFs such as ZNF792, SMAD1, and SMAD7 were differentially correlated in the asthmatic ASM. Additionally, the DEGs, TFs, and differentially connected genes over-represented in the pathways involved with herpes simplex virus infection, Hippo and TGF-β signaling, adherens junctions, gap junctions, and ferroptosis. The rewiring of major regulators unveiled in this study likely modulates the expression of gene-targets as an adaptive response to asthma. These multiple gene interactions pointed out novel targets and pathways for asthma exacerbations.
format	article
author	Priyanka Banerjee Premanand Balraj Nilesh Sudhakar Ambhore Sarah A. Wicher Rodney D. Britt Christina M. Pabelick Y. S. Prakash Venkatachalem Sathish
author_facet	Priyanka Banerjee Premanand Balraj Nilesh Sudhakar Ambhore Sarah A. Wicher Rodney D. Britt Christina M. Pabelick Y. S. Prakash Venkatachalem Sathish
author_sort	Priyanka Banerjee
title	Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
title_short	Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
title_full	Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
title_fullStr	Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
title_full_unstemmed	Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
title_sort	network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8b34563885034ee5adaba98fb6aef59d
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_version_	1718384361454174208

Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma

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