Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3

Diabetic nephropathy (DN), a common diabetes-related complication, is the leading cause of progressive chronic kidney disease (CKD) and end-stage renal disease. Despite the rapid development in the treatment of DN, currently available therapies used in early DN cannot prevent progressive CKD. The ex...

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Main Authors:	Wang, Juan, Cui, Chunli, Fu, Li, Xiao, Zili, Xie, Nanzi, Liu, Yang, Yu, Lu, Wang, Haifeng, Luo, Bangzhen
Format:	Online
Language:	English
Published:	D.A. Spandidos 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940079/

id	pubmed-4940079
recordtype	oai_dc
spelling	pubmed-49400792016-07-21 Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3 Wang, Juan Cui, Chunli Fu, Li Xiao, Zili Xie, Nanzi Liu, Yang Yu, Lu Wang, Haifeng Luo, Bangzhen Articles Diabetic nephropathy (DN), a common diabetes-related complication, is the leading cause of progressive chronic kidney disease (CKD) and end-stage renal disease. Despite the rapid development in the treatment of DN, currently available therapies used in early DN cannot prevent progressive CKD. The exact pathogenic mechanisms and the molecular events underlying DN development remain unclear. Ginsenoside Rg3 is a herbal medicine with numerous pharmacological effects. To gain a greater understanding of the molecular mechanism and signaling pathway underlying the effect of ginsenoside Rg3 in DN therapy, an RNA sequencing approach was performed to screen differential gene expression in a rat model of DN treated with ginsenoside Rg3. A combined bioinformatics analysis was then conducted to obtain insights into the underlying molecular mechanisms of the disease development, in order to identify potential novel targets for the treatment of DN. Six Sprague-Dawley male rats were randomly divided into 3 groups: Normal control group, DN group and ginsenoside-Rg3 treatment group, with two rats in each group. RNA sequencing was adopted for transcriptome profiling of cells from the renal cortex of DN rat model. Differentially expressed genes were screened out. Cluster analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to analyze the differentially expressed genes. In total, 78 differentially expressed genes in the DN control group were identified when compared with the normal control group, of which 52 genes were upregulated and 26 genes were downregulated. Differential expression of 43 genes was observed in the ginsenoside-Rg3 treatment group when compared with the DN control group, consisting of 10 upregulated genes and 33 downregulated genes. Notably, 21 that were downregulated in the DN control group compared with the control were then shown to be upregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. In addition, 7 upregulated genes in the DN control group compared with the control were then shown to be downregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. Cluster analysis based on differentially expressed genes indicated that the transcriptomes are quite different among the samples. Distinct GO terms associated with these groups of genes were shown to be enriched. KEGG pathway analysis demonstrated that differentially expressed genes were predominantly involved in the fatty acid metabolism pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. To the best of our knowledge, this study was the first to present whole genome expression profiling in DN with ginsenoside-Rg3 treatment by RNA-Seq. A set of differentially expressed genes and pathways were identified. These data provided an insight into understanding the molecular mechanisms underlying the effect of ginsenoside-Rg3 treatment of DN. D.A. Spandidos 2016-08 2016-05-27 /pmc/articles/PMC4940079/ /pubmed/27279428 http://dx.doi.org/10.3892/mmr.2016.5349 Text en Copyright: © Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Wang, Juan Cui, Chunli Fu, Li Xiao, Zili Xie, Nanzi Liu, Yang Yu, Lu Wang, Haifeng Luo, Bangzhen
spellingShingle	Wang, Juan Cui, Chunli Fu, Li Xiao, Zili Xie, Nanzi Liu, Yang Yu, Lu Wang, Haifeng Luo, Bangzhen Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
author_facet	Wang, Juan Cui, Chunli Fu, Li Xiao, Zili Xie, Nanzi Liu, Yang Yu, Lu Wang, Haifeng Luo, Bangzhen
author_sort	Wang, Juan
title	Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
title_short	Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
title_full	Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
title_fullStr	Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
title_full_unstemmed	Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3
title_sort	genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside rg3
description	Diabetic nephropathy (DN), a common diabetes-related complication, is the leading cause of progressive chronic kidney disease (CKD) and end-stage renal disease. Despite the rapid development in the treatment of DN, currently available therapies used in early DN cannot prevent progressive CKD. The exact pathogenic mechanisms and the molecular events underlying DN development remain unclear. Ginsenoside Rg3 is a herbal medicine with numerous pharmacological effects. To gain a greater understanding of the molecular mechanism and signaling pathway underlying the effect of ginsenoside Rg3 in DN therapy, an RNA sequencing approach was performed to screen differential gene expression in a rat model of DN treated with ginsenoside Rg3. A combined bioinformatics analysis was then conducted to obtain insights into the underlying molecular mechanisms of the disease development, in order to identify potential novel targets for the treatment of DN. Six Sprague-Dawley male rats were randomly divided into 3 groups: Normal control group, DN group and ginsenoside-Rg3 treatment group, with two rats in each group. RNA sequencing was adopted for transcriptome profiling of cells from the renal cortex of DN rat model. Differentially expressed genes were screened out. Cluster analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to analyze the differentially expressed genes. In total, 78 differentially expressed genes in the DN control group were identified when compared with the normal control group, of which 52 genes were upregulated and 26 genes were downregulated. Differential expression of 43 genes was observed in the ginsenoside-Rg3 treatment group when compared with the DN control group, consisting of 10 upregulated genes and 33 downregulated genes. Notably, 21 that were downregulated in the DN control group compared with the control were then shown to be upregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. In addition, 7 upregulated genes in the DN control group compared with the control were then shown to be downregulated in the ginsenoside-Rg3 treatment group compared with the DN control group. Cluster analysis based on differentially expressed genes indicated that the transcriptomes are quite different among the samples. Distinct GO terms associated with these groups of genes were shown to be enriched. KEGG pathway analysis demonstrated that differentially expressed genes were predominantly involved in the fatty acid metabolism pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. To the best of our knowledge, this study was the first to present whole genome expression profiling in DN with ginsenoside-Rg3 treatment by RNA-Seq. A set of differentially expressed genes and pathways were identified. These data provided an insight into understanding the molecular mechanisms underlying the effect of ginsenoside-Rg3 treatment of DN.
publisher	D.A. Spandidos
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940079/
_version_	1613607115145871360

Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3

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