An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis

Abstract In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology appr...

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Autores principales:	Negin Sheybani, Mohammad Reza Bakhtiarizadeh, Abdolreza Salehi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e5104feb283d4e7e8dc8e51b8b08a60d
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spelling	oai:doaj.org-article:e5104feb283d4e7e8dc8e51b8b08a60d2021-12-02T19:12:35ZAn integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis10.1038/s41598-021-97319-y2045-2322https://doaj.org/article/e5104feb283d4e7e8dc8e51b8b08a60d2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97319-yhttps://doaj.org/toc/2045-2322Abstract In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology approach was used to better understand the molecular mechanisms underlying the development of endometritis. Forty transcriptomic datasets comprising of 20 RNA-Seq (GSE66825) and 20 miRNA-Seq (GSE66826) were obtained from the GEO database. Next, the co-expressed modules were constructed based on RNA-Seq (Rb-modules) and miRNA-Seq (mb-modules) data, separately, using a weighted gene co-expression network analysis (WGCNA) approach. Preservation analysis was used to find the non-preserved Rb-modules in endometritis samples. Afterward, the non-preserved Rb-modules were assigned to the mb-modules to construct the integrated regulatory networks. Just highly connected genes (hubs) in the networks were considered and functional enrichment analysis was used to identify the biological pathways associated with the development of the disease. Furthermore, additional bioinformatic analysis including protein–protein interactions network and miRNA target prediction were applied to enhance the reliability of the results. Thirty-five Rb-modules and 10 mb-modules were identified and 19 and 10 modules were non-preserved, respectively, which were enriched in biological pathways related to endometritis like inflammation and ciliogenesis. Two non-preserved Rb-modules were significantly assigned to three mb-modules and three and two important sub-networks in the Rb-modules were identified, respectively, including important mRNAs, lncRNAs and miRNAs genes like IRAK1, CASP3, CCDC40, CCDC39, ZMYND10, FOXJ1, TLR4, IL10, STAT3, FN1, AKT1, CD68, ENSBTAG00000049936, ENSBTAG00000050527, ENSBTAG00000051242, ENSBTAG00000049287, bta-miR-449, bta-miR-484, bta-miR-149, bta-miR-30b and bta-miR-423. The potential roles of these genes have been previously demonstrated in endometritis or related pathways, which reinforced putative functions of the suggested integrated regulatory networks in the endometritis pathogenesis. These findings may help further elucidate the underlying mechanisms of bovine endometritis.Negin SheybaniMohammad Reza BakhtiarizadehAbdolreza SalehiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-19 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Negin Sheybani Mohammad Reza Bakhtiarizadeh Abdolreza Salehi An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
description	Abstract In dairy cattle, endometritis is a severe infectious disease that occurs following parturition. It is clear that genetic factors are involved in the etiology of endometritis, however, the molecular pathogenesis of endometritis is not entirely understood. In this study, a system biology approach was used to better understand the molecular mechanisms underlying the development of endometritis. Forty transcriptomic datasets comprising of 20 RNA-Seq (GSE66825) and 20 miRNA-Seq (GSE66826) were obtained from the GEO database. Next, the co-expressed modules were constructed based on RNA-Seq (Rb-modules) and miRNA-Seq (mb-modules) data, separately, using a weighted gene co-expression network analysis (WGCNA) approach. Preservation analysis was used to find the non-preserved Rb-modules in endometritis samples. Afterward, the non-preserved Rb-modules were assigned to the mb-modules to construct the integrated regulatory networks. Just highly connected genes (hubs) in the networks were considered and functional enrichment analysis was used to identify the biological pathways associated with the development of the disease. Furthermore, additional bioinformatic analysis including protein–protein interactions network and miRNA target prediction were applied to enhance the reliability of the results. Thirty-five Rb-modules and 10 mb-modules were identified and 19 and 10 modules were non-preserved, respectively, which were enriched in biological pathways related to endometritis like inflammation and ciliogenesis. Two non-preserved Rb-modules were significantly assigned to three mb-modules and three and two important sub-networks in the Rb-modules were identified, respectively, including important mRNAs, lncRNAs and miRNAs genes like IRAK1, CASP3, CCDC40, CCDC39, ZMYND10, FOXJ1, TLR4, IL10, STAT3, FN1, AKT1, CD68, ENSBTAG00000049936, ENSBTAG00000050527, ENSBTAG00000051242, ENSBTAG00000049287, bta-miR-449, bta-miR-484, bta-miR-149, bta-miR-30b and bta-miR-423. The potential roles of these genes have been previously demonstrated in endometritis or related pathways, which reinforced putative functions of the suggested integrated regulatory networks in the endometritis pathogenesis. These findings may help further elucidate the underlying mechanisms of bovine endometritis.
format	article
author	Negin Sheybani Mohammad Reza Bakhtiarizadeh Abdolreza Salehi
author_facet	Negin Sheybani Mohammad Reza Bakhtiarizadeh Abdolreza Salehi
author_sort	Negin Sheybani
title	An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
title_short	An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
title_full	An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
title_fullStr	An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
title_full_unstemmed	An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis
title_sort	integrated analysis of mrnas, lncrnas, and mirnas based on weighted gene co-expression network analysis involved in bovine endometritis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e5104feb283d4e7e8dc8e51b8b08a60d
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_version_	1718377030667468800

An integrated analysis of mRNAs, lncRNAs, and miRNAs based on weighted gene co-expression network analysis involved in bovine endometritis

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