Bioinformatics Analysis of Genes and Pathways of CD11b+/Ly6Cintermediate Macrophages after Renal Ischemia-Reperfusion Injury

Sun, Dong; Wan, Xin; Pan, Binbin; Sun, Qing; Ji, Xiaobing; Zhang, Na; Zhang, Hao; Cao, Changchun

doi:10.1007/s11596-018-1848-7

Cited by 8 publications

(9 citation statements)

References 43 publications

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“…Another cohort of RNA sequencing data found that apoptosis, migration, oxidation–reduction, and proliferation of macrophages were involved in I/R injury. Changes in CD11b+/Ly6c macrophages and polarization participated in the process of AKI ( Sun et al, 2018 ). In an I/R AKI mouse model, transcriptome sequencing of renal tubules suggested that metabolic maladaptation was implicated in AKI progression to chronic fibrosis, with massive lipid droplet accumulations observed in renal tubular epithelial cells ( Zhang et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury

Shi

Chen

Teng

2021

Front. Mol. Biosci.

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Acute kidney injury (AKI) is a severe and frequently observed condition associated with high morbidity and mortality. The molecular mechanisms underlying AKI have not been elucidated due to the complexity of the pathophysiological processes. Thus, we investigated the key biological molecules contributing to AKI based on the transcriptome profile. We analyzed the RNA sequencing data from 39 native human renal biopsy samples and 9 reference nephrectomies from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and Gene Ontology (GO) analysis revealed that various GO terms were dysregulated in AKI. Gene set enrichment analysis (GSEA) highlighted dysregulated pathways, including “DNA replication,” “chemokine signaling pathway,” and “metabolic pathways.” Furthermore, the protein-to-protein interaction (PPI) networks of the DEGs were constructed, and the hub genes were identified using Cytoscape. Moreover, weighted gene co-expression network analysis (WGCNA) was performed to validate the DEGs in AKI-related modules. Subsequently, the upregulated hub genes STUB1, SOCS1, and VHL were validated as upregulated in human AKI and a mouse cisplatin-induced AKI model. Moreover, the biological functions of STUB1 were investigated in renal tubular epithelial cells. Cisplatin treatment increased STUB1 expression in a dose-dependent manner at both the mRNA and protein levels. Knockdown of STUB1 by siRNA increased the expression of proapoptotic Bax and cleaved caspase-3 while decreasing antiapoptotic Bcl-2. In addition, silencing STUB1 increased the apoptosis of HK-2 cells and the proinflammatory cytokine production of IL6, TNFα, and IL1β induced by cisplatin. These results indicated that STUB1 may contribute to the initiation and progression of AKI by inducing renal tubular epithelial cell apoptosis and renal inflammation.

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Section: Introductionmentioning

confidence: 99%

Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury

Shi

Chen

Teng

2021

Front. Mol. Biosci.

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“…The RPS5 was closely related to transcription elongation factor-3 and DNA connection protein II, and its expression was highly conserved [47,[57][58][59][60][61][62][63]. RPS18, a highly conserved member of the nuclear protein S13 superfamily, is one of the constituent proteins of the eukaryotic ribosomal 40S subunit, and stably expressed in different tissues [34,[64][65][66][67][68]. Therefore, with the high expression level and best stability, we selected RPS5 and RPS18 as the suitable reference genes in the polyploid of Cyprinus carpio and Carassius auratus.…”

Section: Discussionmentioning

confidence: 99%

Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Liu

Yuan

et al. 2020

BMC Genet

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Background Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to answer whether the expression of reported traditional reference genes changes or not in the polyploid fish Results By retrieving the mRNA sequencing data of three different ploidy fish from the NCBI SRA database, we selected 12 candidate reference genes, and examined their expression levels in the 10 tissues and in the four cell lines of three different ploidy fish by real-time PCR. Then, the expression profiles of these 12 candidate reference genes were systematically evaluated by using the software platforms: BestKeeper, NormFinder and geNorm. Conclusion The 28S ribosomal protein S5 gene (RPS5) and the ribosomal protein S18 gene (RPS18) are the most suitable reference genes for the polyploid of Cyprinus carpio and Carassius auratus, demonstrated by both of the tissues and the cultured cells.

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“…TTD and OMIM databases were searched for "cancer" and "neoplast" to identify the genes related to tumor development [18][19]. Retrieved data were merged, duplicates were removed, and the intersection of the chemical targets was obtained using the Funrich platform [20]. Venn diagrams were constructed to reveal the key anticancer targets of rhubarb.…”

Section: Assessment Of Disease Targetsmentioning

confidence: 99%

Network Pharmacology Analysis of the active components and anticancer targets of Rhubarb

2021

Preprint

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To investigate the mechanisms and active components governing the anticancer activity of rhubarb.The TCMSP database was screened to identify the active components of rhubarb and Swiss target predictions were generated to predict their cellular targets. TTD and OMIM databases were used to predict tumor-related target genes. "Cytoscape" was used to construct drug targets. PPI network analysis, GO enrichment analysis and KEGG pathway analysis of the key targets were investigated using String and David databases. A total of 33 components and 116 corresponding targets were screened. Amongst them, the key active compounds in rhubarb included emodin, aloe emodin, β-sitosterol, emodin methyl ether and rhein, which were predicted to target TP53, AKT1, STAT3, PIK3CA, HRAS, and VEGFA. GO analysis revealed that the cellular targets clustered into 159 biological processes, including those involved in cellular composition (n=24) and molecular functions (n=42, P<0.01). KEGG pathway analysis revealed 85 (P < 0.01) pathways related to cancer. The active compounds in rhubarb target TP53, AKT1 and PIK3CA. Rhubarb therefore regulates cancer development through an array of biological pathways.

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Bioinformatics Analysis of Genes and Pathways of CD11b+/Ly6Cintermediate Macrophages after Renal Ischemia-Reperfusion Injury

Cited by 8 publications

References 43 publications

Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury

Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury

Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Network Pharmacology Analysis of the active components and anticancer targets of Rhubarb

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