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Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is one of the world’s leading causes of death and a major chronic disease, highly prevalent in the aging population exposed to tobacco smoke and airborne pollutants, which calls for early and useful biomolecular predictors. Roles of noncoding...

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Autores principales: Liu, Pengcheng, Wang, Yucong, Zhang, Ningning, Zhao, Xiaomin, Li, Renming, Wang, Yu, Chen, Chen, Wang, Dandan, Zhang, Xiaoming, Chen, Liang, Zhao, Dahai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9188256/
https://www.ncbi.nlm.nih.gov/pubmed/35690768
http://dx.doi.org/10.1186/s12931-022-02069-8
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author Liu, Pengcheng
Wang, Yucong
Zhang, Ningning
Zhao, Xiaomin
Li, Renming
Wang, Yu
Chen, Chen
Wang, Dandan
Zhang, Xiaoming
Chen, Liang
Zhao, Dahai
author_facet Liu, Pengcheng
Wang, Yucong
Zhang, Ningning
Zhao, Xiaomin
Li, Renming
Wang, Yu
Chen, Chen
Wang, Dandan
Zhang, Xiaoming
Chen, Liang
Zhao, Dahai
author_sort Liu, Pengcheng
collection PubMed
description BACKGROUND: Chronic obstructive pulmonary disease (COPD) is one of the world’s leading causes of death and a major chronic disease, highly prevalent in the aging population exposed to tobacco smoke and airborne pollutants, which calls for early and useful biomolecular predictors. Roles of noncoding RNAs in COPD have been proposed, however, not many studies have systematically investigated the crosstalk among various transcripts in this context. The construction of RNA functional networks such as lncRNA-mRNA, and circRNA-miRNA-mRNA interaction networks could therefore facilitate our understanding of RNA interactions in COPD. Here, we identified the expression of RNA transcripts in RNA sequencing from COPD patients, and the potential RNA networks were further constructed. METHODS: All fresh peripheral blood samples of three patients with COPD and three non-COPD patients were collected and examined for mRNA, miRNA, lncRNA, and circRNA expression followed by qRT-PCR validation. We also examined mRNA expression to enrich relevant biological pathways. lncRNA-mRNA coexpression network and circRNA-miRNA-mRNA network in COPD were constructed. RESULTS: In this study, we have comprehensively identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. 282 mRNAs, 146 lncRNAs, 85 miRNAs, and 81 circRNAs were differentially expressed. GSEA analysis showed that these differentially expressed RNAs correlate with several critical biological processes such as “ncRNA metabolic process”, “ncRNA processing”, “ribosome biogenesis”, “rRNAs metabolic process”, “tRNA metabolic process” and “tRNA processing”, which might be participating in the progression of COPD. RT-qPCR with more clinical COPD samples was used for the validation of some differentially expressed RNAs, and the results were in high accordance with the RNA sequencing. Given the putative regulatory function of lncRNAs and circRNAs, we have constructed the co-expression network between lncRNA and mRNA. To demonstrate the potential interactions between circRNAs and miRNAs, we have also constructed a competing endogenous RNA (ceRNA) network of differential expression circRNA-miRNA-mRNA in COPD. CONCLUSIONS: In this study, we have identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs, providing a systematic view of the differentially expressed RNA in the context of COPD. We have also constructed the lncRNA-mRNA co-expression network, and for the first time constructed the circRNA-miRNA-mRNA in COPD. This study reveals the RNA involvement and potential regulatory roles in COPD, and further uncovers the interactions among those RNAs, which will assist the pathological investigations of COPD and shed light on therapeutic targets exploration for COPD. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-022-02069-8.
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spelling pubmed-91882562022-06-12 Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease Liu, Pengcheng Wang, Yucong Zhang, Ningning Zhao, Xiaomin Li, Renming Wang, Yu Chen, Chen Wang, Dandan Zhang, Xiaoming Chen, Liang Zhao, Dahai Respir Res Research BACKGROUND: Chronic obstructive pulmonary disease (COPD) is one of the world’s leading causes of death and a major chronic disease, highly prevalent in the aging population exposed to tobacco smoke and airborne pollutants, which calls for early and useful biomolecular predictors. Roles of noncoding RNAs in COPD have been proposed, however, not many studies have systematically investigated the crosstalk among various transcripts in this context. The construction of RNA functional networks such as lncRNA-mRNA, and circRNA-miRNA-mRNA interaction networks could therefore facilitate our understanding of RNA interactions in COPD. Here, we identified the expression of RNA transcripts in RNA sequencing from COPD patients, and the potential RNA networks were further constructed. METHODS: All fresh peripheral blood samples of three patients with COPD and three non-COPD patients were collected and examined for mRNA, miRNA, lncRNA, and circRNA expression followed by qRT-PCR validation. We also examined mRNA expression to enrich relevant biological pathways. lncRNA-mRNA coexpression network and circRNA-miRNA-mRNA network in COPD were constructed. RESULTS: In this study, we have comprehensively identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs in peripheral blood of COPD patients with high-throughput RNA sequencing. 282 mRNAs, 146 lncRNAs, 85 miRNAs, and 81 circRNAs were differentially expressed. GSEA analysis showed that these differentially expressed RNAs correlate with several critical biological processes such as “ncRNA metabolic process”, “ncRNA processing”, “ribosome biogenesis”, “rRNAs metabolic process”, “tRNA metabolic process” and “tRNA processing”, which might be participating in the progression of COPD. RT-qPCR with more clinical COPD samples was used for the validation of some differentially expressed RNAs, and the results were in high accordance with the RNA sequencing. Given the putative regulatory function of lncRNAs and circRNAs, we have constructed the co-expression network between lncRNA and mRNA. To demonstrate the potential interactions between circRNAs and miRNAs, we have also constructed a competing endogenous RNA (ceRNA) network of differential expression circRNA-miRNA-mRNA in COPD. CONCLUSIONS: In this study, we have identified and analyzed the differentially expressed mRNAs, lncRNAs, miRNAs, and circRNAs, providing a systematic view of the differentially expressed RNA in the context of COPD. We have also constructed the lncRNA-mRNA co-expression network, and for the first time constructed the circRNA-miRNA-mRNA in COPD. This study reveals the RNA involvement and potential regulatory roles in COPD, and further uncovers the interactions among those RNAs, which will assist the pathological investigations of COPD and shed light on therapeutic targets exploration for COPD. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-022-02069-8. BioMed Central 2022-06-11 2022 /pmc/articles/PMC9188256/ /pubmed/35690768 http://dx.doi.org/10.1186/s12931-022-02069-8 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Liu, Pengcheng
Wang, Yucong
Zhang, Ningning
Zhao, Xiaomin
Li, Renming
Wang, Yu
Chen, Chen
Wang, Dandan
Zhang, Xiaoming
Chen, Liang
Zhao, Dahai
Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title_full Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title_fullStr Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title_full_unstemmed Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title_short Comprehensive identification of RNA transcripts and construction of RNA network in chronic obstructive pulmonary disease
title_sort comprehensive identification of rna transcripts and construction of rna network in chronic obstructive pulmonary disease
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9188256/
https://www.ncbi.nlm.nih.gov/pubmed/35690768
http://dx.doi.org/10.1186/s12931-022-02069-8
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