Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis

Abstract Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal (GI) tract. Ulcerative colitis (UC) is a type of IBD. Pregnane X Receptor (PXR) is a member of the nuclear receptor superfamily. In order to deepen understanding and exploration of the mole...

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Autores principales:	Hanze Guo, Yan Chi, Naiyu Chi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/bd2a730e631a443eb41e9ee2dc33d272
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spelling	oai:doaj.org-article:bd2a730e631a443eb41e9ee2dc33d2722021-12-02T13:33:44ZBioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis10.1038/s41598-021-83742-82045-2322https://doaj.org/article/bd2a730e631a443eb41e9ee2dc33d2722021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83742-8https://doaj.org/toc/2045-2322Abstract Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal (GI) tract. Ulcerative colitis (UC) is a type of IBD. Pregnane X Receptor (PXR) is a member of the nuclear receptor superfamily. In order to deepen understanding and exploration of the molecular mechanism of regulation roles of PXR on UC, biological informatics analysis was performed. First, 878 overlapping differentially expressed genes (DEGs) between UC and normal samples were obtained from the Gene Expression Omnibus (GEO) database (GSE59071 and GSE38713) by using the "limma" R language package. Then WGCNA analysis was performed by 878 DEGs to obtain co-expression modules that were positively and negatively correlated with clinical traits. GSEA analysis of PXR results obtained the signal pathways enriched in the PXR high and low expression group and the active genes of each signal pathway. Then the association of PXR with genes that are both active in high expression group and negatively related to diseases (gene set 1), or both active in low expression group and negatively related to diseases (gene set 2) was analyzed by String database. Finally, carboxylesterase 2 (CES2), ATP binding cassette subfamily G member 2 (ABCG2), phosphoenolpyruvate carboxykinase (PCK1), PPARG coactivator 1 alpha (PPARGC1A), cytochrome P450 family 2 subfamily B member 6 (CYP2B6) from gene set 1 and C-X-C motif chemokine ligand 8 (CXCL8) from gene set 2 were screened out. After the above analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) verification, we speculated that PXR may exert a protective role on UC by promoting CES2, ABCG2, PCK1, PPARGC1A, CYP2B6 expression and inhibiting CXCL8 expression in their corresponding signal pathway in intestinal tissue.Hanze GuoYan ChiNaiyu ChiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hanze Guo Yan Chi Naiyu Chi Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
description	Abstract Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal (GI) tract. Ulcerative colitis (UC) is a type of IBD. Pregnane X Receptor (PXR) is a member of the nuclear receptor superfamily. In order to deepen understanding and exploration of the molecular mechanism of regulation roles of PXR on UC, biological informatics analysis was performed. First, 878 overlapping differentially expressed genes (DEGs) between UC and normal samples were obtained from the Gene Expression Omnibus (GEO) database (GSE59071 and GSE38713) by using the "limma" R language package. Then WGCNA analysis was performed by 878 DEGs to obtain co-expression modules that were positively and negatively correlated with clinical traits. GSEA analysis of PXR results obtained the signal pathways enriched in the PXR high and low expression group and the active genes of each signal pathway. Then the association of PXR with genes that are both active in high expression group and negatively related to diseases (gene set 1), or both active in low expression group and negatively related to diseases (gene set 2) was analyzed by String database. Finally, carboxylesterase 2 (CES2), ATP binding cassette subfamily G member 2 (ABCG2), phosphoenolpyruvate carboxykinase (PCK1), PPARG coactivator 1 alpha (PPARGC1A), cytochrome P450 family 2 subfamily B member 6 (CYP2B6) from gene set 1 and C-X-C motif chemokine ligand 8 (CXCL8) from gene set 2 were screened out. After the above analysis and reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) verification, we speculated that PXR may exert a protective role on UC by promoting CES2, ABCG2, PCK1, PPARGC1A, CYP2B6 expression and inhibiting CXCL8 expression in their corresponding signal pathway in intestinal tissue.
format	article
author	Hanze Guo Yan Chi Naiyu Chi
author_facet	Hanze Guo Yan Chi Naiyu Chi
author_sort	Hanze Guo
title	Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
title_short	Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
title_full	Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
title_fullStr	Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
title_full_unstemmed	Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis
title_sort	bioinformatis analysis reveals possible molecular mechanism of pxr on regulating ulcerative colitis
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/bd2a730e631a443eb41e9ee2dc33d272
work_keys_str_mv	AT hanzeguo bioinformatisanalysisrevealspossiblemolecularmechanismofpxronregulatingulcerativecolitis AT yanchi bioinformatisanalysisrevealspossiblemolecularmechanismofpxronregulatingulcerativecolitis AT naiyuchi bioinformatisanalysisrevealspossiblemolecularmechanismofpxronregulatingulcerativecolitis
_version_	1718392879834988544

Bioinformatis analysis reveals possible molecular mechanism of PXR on regulating ulcerative colitis

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