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Huang B, Li J, Zhao J. Screening and identification of potential biomarkers and therapeutic targets for systemic sclerosis-associated interstitial lung disease. Arch Rheumatol 2022; 36:548-559. [PMID: 35382367 PMCID: PMC8957772 DOI: 10.46497/archrheumatol.2021.8625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/18/2021] [Indexed: 11/03/2022] Open
Abstract
Objectives This study aims to analyze gene expression in lung tissue and lung fibroblasts of patients with systemic sclerosis-associated interstitial lung disease (SSc-ILD) to identify potential biomarkers and therapeutic targets and to examine its possible role in the pathogenesis of SSc-ILD. Patients and methods We obtained datasets from Gene Expression Omnibus (GEO) database, and used Robust Rank Aggregation to calculate the co-expressed differentially-expressed-genes (DEGs) in three chips, then analyzed the function, signaling pathways and the protein-protein interaction network of the DEGs. Finally, we verified the DEGs related to SSc-ILD by three databases of Comparative Toxicogenomics Database (CTD), GENE, and DisGeNET, respectively. Results There were 16 co-expressed DEGs related to SSc-ILD in three GEO series, of which six genes were upregulated, and 10 genes were downregulated. The CTD included 29,936 genes related to SSc, and the GENE and DisGeNET databases had 429 genes related to SSc. Conclusion The results of gene differential expression analysis suggest that interleukin-6, chemokine ligand 2, intercellular adhesion molecule 1, tumor necrosis factor alpha-induced protein 3, pentraxin 3, and cartilage oligomeric matrix protein may be implicated in the pathogenesis of SSc-ILD and are expected to be potential biomarkers and therapeutic targets for SSc-ILD.
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Affiliation(s)
- Biqing Huang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College Hospital, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Jing Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College Hospital, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College Hospital, Beijing, China
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Cheuk YC, Zhang P, Xu S, Wang J, Chen T, Mao Y, Jiang Y, Luo Y, Guo J, Wang W, Rong R. Bioinformatics analysis of pathways of renal infiltrating macrophages in different renal disease models. Transl Androl Urol 2022; 10:4333-4343. [PMID: 35070815 PMCID: PMC8749068 DOI: 10.21037/tau-21-761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background Recent studies have suggested that macrophages are significantly involved in different renal diseases. However, the role of these renal infiltrating macrophages has not been entirely uncovered. To further clarify the underlying mechanism and identify therapeutic targets, a bioinformatic analysis based on transcriptome profiles was performed. Methods Three transcription profiling datasets, GSE27045, GSE51466 and GSE75808, were obtained from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were assessed by Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set enrichment analysis (GSEA). Results The classic signaling pathways and metabolic pathways of macrophages infiltrating the kidney in different pathophysiological processes, including lupus nephritis (LN), renal crystal formation and renal ischemia-reperfusion injury (IRI), were analysed. Furthermore, the common classical pathways significantly altered in the three renal disorders were the oxidative phosphorylation, VEGF signaling and JAK/STAT signaling pathways, while the renin-angiotensin system was uniquely altered in LN, the glycolysis and gluconeogenesis pathways were uniquely altered in models of renal crystal formation, and the calcium signaling pathway was specific to renal IRI. Conclusions Via bioinformatics analysis, this study revealed the transcriptional features of macrophages in murine LN, renal crystal formation and IRI models, which may serve as promising targets for mechanistic research and the clinical treatment of multiple renal diseases.
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Affiliation(s)
- Yin Celeste Cheuk
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Pingbao Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Shihao Xu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Jiyan Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Tian Chen
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Yongxin Mao
- Department of Urology, Huadong Hospital, Fudan University, Shanghai, China
| | - Yamei Jiang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Yongsheng Luo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Jingjing Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
| | - Weixi Wang
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ruiming Rong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Shanghai, China
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Shi Y, Chen G, Teng J. Network-Based Expression Analyses and Experimental Verifications Reveal the Involvement of STUB1 in Acute Kidney Injury. Front Mol Biosci 2021; 8:655361. [PMID: 34262937 PMCID: PMC8273177 DOI: 10.3389/fmolb.2021.655361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
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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Affiliation(s)
- Yanting Shi
- Department of Nephrology, Xiamen Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Genwen Chen
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Teng
- Department of Nephrology, Xiamen Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China
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Liu W, Yuan X, Yuan S, Dai L, Dong S, Liu J, Peng L, Wang M, Tang Y, Xiao Y. Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus. BMC Genet 2020; 21:107. [PMID: 32943013 PMCID: PMC7499967 DOI: 10.1186/s12863-020-00915-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 08/31/2020] [Indexed: 12/29/2022] Open
Abstract
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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Affiliation(s)
- Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Xiudan Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Shuli Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Liuye Dai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Shenghua Dong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Minmeng Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Yi Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
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Luo J, Li H, Liu Z, Li C, Wang R, Fang J, Lu S, Guo J, Zhu X, Wang X. Integrative analyses of gene expression profile reveal potential crucial roles of mitotic cell cycle and microtubule cytoskeleton in pulmonary artery hypertension. BMC Med Genomics 2020; 13:86. [PMID: 32586319 PMCID: PMC7318763 DOI: 10.1186/s12920-020-00740-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 06/15/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is a life-threatening condition. The aim of this study was to explore potential crucial genes and pathways associated with PAH based on integrative analyses of gene expression and to shed light on the identification of biomarker for PAH. METHODS Gene expression profile of pulmonary tissues from 27 PAH patients and 22 normal controls were downloaded from public database (GSE53408 and GSE113439). After the identification of differentially expressed genes (DEGs), hub pathways and genes were identified based on the comprehensive evaluation of protein-protein interaction (PPI) network analysis, modular analysis and cytohubba's analysis, and further validated in another PAH transcriptomic dataset (GSE33463). Potentially associated micro-RNAs (miRNAs) were also predicted. RESULTS A total of 521 DEGs were found between PAH and normal controls, including 432 up-regulated DEGs and 89 down-regulated DEGs. Functional enrichment analysis showed that these DEGs were mainly enriched in mitotic cell cycle process, mitotic cell cycle and microtubule cytoskeleton organization. Moreover, five key genes (CDK1, SMC2, SMC4, KIF23, and CENPE) were identified and then further validated in another transcriptomic dataset associated with special phenotypes of PAH. Furthermore, these hub genes were mainly enriched in promoting mitotic cell cycle process, which may be closely associated with the pathogenesis of PAH. We also found that the predicted miRNAs targeting these hub genes were found to be enriched in TGF-β and Hippo signaling pathway. CONCLUSION These findings are expected to gain a further insight into the development of PAH and provide a promising index for the detection of PAH.
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Affiliation(s)
- Jing Luo
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Haiyan Li
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Chenlu Li
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinxia Fang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Jing Guo
- College of psychologic medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaochun Zhu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiaobing Wang
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, China.
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