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Zhu X, Jiang L, Yang H, Chen T, Wu X, Lv K. Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. Cancer Cell Int 2020; 20:393. [PMID: 32821246 PMCID: PMC7429694 DOI: 10.1186/s12935-020-01488-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/07/2020] [Indexed: 02/08/2023] Open
Abstract
Background Glioblastoma multiforme (GBM) is the most seriously brain tumor with extremely poor prognosis. Recent research has demonstrated that competitive endogenous RNA (ceRNA) network which long noncoding RNAs (lncRNAs) act as microRNA (miRNA) sponges to regulate mRNA expression were closely related to tumor development. However, the regulatory mechanisms and functional roles of ceRNA network in the pathogenesis of GBM are remaining poorly understood. Methods In this study, we systematically analyzed the expression profiles of lncRNA and mRNA (GSE51146 dataset) and miRNA (GSE65626 dataset) from GEO database. Then, we constructed a ceRNA network with the dysregulated genes by bioinformatics methods. The TCGA and GSE4290 dataset were used to confirm the expression and prognostic value of candidate mRNAs. Results In total, 3413 differentially expressed lncRNAs and mRNAs, 305 differentially expressed miRNAs were indentified in GBM samples. Then a ceRNA network containing 3 lncRNAs, 5 miRNAs, and 60 mRNAs was constructed. The overall survival analysis of TCGA databases indicated that two mRNAs (C1s and HSD3B7) were remarkly related with the prognosis of GBM. Conclusion The ceRNA network may increase our understanding to the pathogenesis of GBM. In general, the candidate mRNAs from the ceRNA network can be predicted as new therapeutic targets and prognostic biomarkers for GBM.
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Affiliation(s)
- Xiaolong Zhu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Hui Yang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Tianbing Chen
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Xingwei Wu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
| | - Kun Lv
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu, 241001 People's Republic of China.,Non-coding RNA Research Center of Wannan Medical College, Wuhu, 241001 China.,Central Laboratory of Yijishan Hospital, Wannan Medical College, Wuhu, 241001 People's Republic of China
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C1r/C1s deficiency is insufficient to induce murine systemic lupus erythematosus. Genes Immun 2018; 20:121-130. [PMID: 29550838 DOI: 10.1038/s41435-018-0020-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/14/2018] [Accepted: 01/18/2018] [Indexed: 11/08/2022]
Abstract
C1s deficiency is strongly associated with the development of human systemic lupus erythematosus (SLE); however, the mechanisms by which C1s deficiency contributes to the development of SLE have not yet been elucidated in detail. Using ICR-derived-glomerulonephritis (ICGN) mouse strain that develops SLE and very weakly expresses C1s in the liver, we investigated the protective roles of C1s against SLE. A genetic sequence analysis revealed complete deletion of the C1s1 gene, a mouse homolog of the human C1s gene, with partial deletion of the C1ra and C1rb genes in the ICGN strain. This deletion led to the absence of C1r/C1s and a low level of C1q in the circulation. In order to investigate whether the C1r/C1s deficiency induces SLE, we produced a congenic mouse strain by introducing the deletion region of ICGN into the C57BL/6 strain. Congenic mice exhibited no C1r/C1s and a low level of C1q in the circulation, but did not have any autoimmune defects. These results suggest that C1r/C1s deficiency is not sufficient to drive murine SLE and also that other predisposing genes exist in ICGN mice.
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Malas TB, Formica C, Leonhard WN, Rao P, Granchi Z, Roos M, Peters DJM, 't Hoen PAC. Meta-analysis of polycystic kidney disease expression profiles defines strong involvement of injury repair processes. Am J Physiol Renal Physiol 2017; 312:F806-F817. [PMID: 28148532 DOI: 10.1152/ajprenal.00653.2016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/30/2017] [Accepted: 01/30/2017] [Indexed: 12/25/2022] Open
Abstract
Polycystic kidney disease (PKD) is a major cause of end-stage renal disease. The disease mechanisms are not well understood and the pathogenesis toward renal failure remains elusive. In this study, we present the first RNASeq analysis of a Pkd1-mutant mouse model in a combined meta-analysis with other published PKD expression profiles. We introduce the PKD Signature, a set of 1,515 genes that are commonly dysregulated in PKD studies. We show that the signature genes include many known and novel PKD-related genes and functions. Moreover, genes with a role in injury repair, as evidenced by expression data and/or automated literature analysis, were significantly enriched in the PKD Signature, with 35% of the PKD Signature genes being directly implicated in injury repair. NF-κB signaling, epithelial-mesenchymal transition, inflammatory response, hypoxia, and metabolism were among the most prominent injury or repair-related biological processes with a role in the PKD etiology. Novel PKD genes with a role in PKD and in injury were confirmed in another Pkd1-mutant mouse model as well as in animals treated with a nephrotoxic agent. We propose that compounds that can modulate the injury-repair response could be valuable drug candidates for PKD treatment.
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Affiliation(s)
- Tareq B Malas
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
| | - Chiara Formica
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
| | - Wouter N Leonhard
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
| | | | | | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
| | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; and
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