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Feng C, Wang Z, Liu C, Liu S, Wang Y, Zeng Y, Wang Q, Peng T, Pu X, Liu J. Integrated bioinformatical analysis, machine learning and in vitro experiment-identified m6A subtype, and predictive drug target signatures for diagnosing renal fibrosis. Front Pharmacol 2022; 13:909784. [PMID: 36120336 PMCID: PMC9470879 DOI: 10.3389/fphar.2022.909784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Renal biopsy is the gold standard for defining renal fibrosis which causes calcium deposits in the kidneys. Persistent calcium deposition leads to kidney inflammation, cell necrosis, and is related to serious kidney diseases. However, it is invasive and involves the risk of complications such as bleeding, especially in patients with end-stage renal diseases. Therefore, it is necessary to identify specific diagnostic biomarkers for renal fibrosis. This study aimed to develop a predictive drug target signature to diagnose renal fibrosis based on m6A subtypes. We then performed an unsupervised consensus clustering analysis to identify three different m6A subtypes of renal fibrosis based on the expressions of 21 m6A regulators. We evaluated the immune infiltration characteristics and expression of canonical immune checkpoints and immune-related genes with distinct m6A modification patterns. Subsequently, we performed the WGCNA analysis using the expression data of 1,611 drug targets to identify 474 genes associated with the m6A modification. 92 overlapping drug targets between WGCNA and DEGs (renal fibrosis vs. normal samples) were defined as key drug targets. A five target gene predictive model was developed through the combination of LASSO regression and stepwise logistic regression (LASSO-SLR) to diagnose renal fibrosis. We further performed drug sensitivity analysis and extracellular matrix analysis on model genes. The ROC curve showed that the risk score (AUC = 0.863) performed well in diagnosing renal fibrosis in the training dataset. In addition, the external validation dataset further confirmed the outstanding predictive performance of the risk score (AUC = 0.755). These results indicate that the risk model has an excellent predictive performance for diagnosing the disease. Furthermore, our results show that this 5-target gene model is significantly associated with many drugs and extracellular matrix activities. Finally, the expression levels of both predictive signature genes EGR1 and PLA2G4A were validated in renal fibrosis and adjacent normal tissues by using qRT-PCR and Western blot method.
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Affiliation(s)
- Chunxiang Feng
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong Guangzhou, Wuhan, China
| | - Zhixian Wang
- Department of Urology, Wuhan Hospital of Traditional Chinese and Western Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Urology, Wuhan No. 1 Hospital, Wuhan, China
| | - Chang Liu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiliang Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxi Wang
- Department of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zeng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Qianqian Wang
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong Guangzhou, Wuhan, China
| | - Tianming Peng
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong Guangzhou, Wuhan, China
| | - Xiaoyong Pu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong Guangzhou, Wuhan, China
- *Correspondence: Xiaoyong Pu, ; Jiumin Liu,
| | - Jiumin Liu
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong Guangzhou, Wuhan, China
- *Correspondence: Xiaoyong Pu, ; Jiumin Liu,
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Wang R, Si L, Zhu D, Shen G, Long Q, Zhao Y. Genetic variants in GHR and PLCE1 genes are associated with susceptibility to esophageal cancer. Mol Genet Genomic Med 2020; 8:e1474. [PMID: 32869542 PMCID: PMC7549587 DOI: 10.1002/mgg3.1474] [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: 04/28/2020] [Revised: 07/13/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022] Open
Abstract
Background Esophageal cancer (EC) is the leading cause of cancer‐related mortality worldwide. The underlying genetic risk factors remain unclear. The association between gene growth hormone receptor (GHR) and phospholipase C epsilon 1 (PLCE1) polymorphisms and the EC risk were identified in this study. Methods A total of 506 EC cases and 507 controls were included in this research. Two SNPs (rs6898743 of GHR and rs2274223 of PLCE1) were selected and genotyped. The associations between gene polymorphisms and the EC risk were assessed by logistic regression analysis. The databases RegulomeDB, GTEx, and UALCAN were used for functional annotations. Results In the allelic frequencies analysis, the rs6898743 of GHR was associated with decreased susceptibility of EC (OR = 0.83, 95% CI: 0.70–1.00, p = 0.049), while rs2274223 of PLCE1 was associated with increased 0.25‐fold EC risk (OR = 1.25, 95% CI: 1.02–1.53, p = 0.037). The “GC” genotype of rs6898743 was associated with a 0.24‐fold decreased risk of EC under co‐dominant model (OR = 0.76, 95% CI: 0.58–0.99, p = 0.046), and the “GA” genotype of rs2274223 was associated with increased EC risk under co‐dominant model (OR = 1.36, 95% CI: 1.04–1.77, p = 0.023). Using GTEx database, rs2274223 was found to be significant associated with increased PLCE1 expression (p = 4.1 × 10−7) in esophagus muscularis. The UALCAN database demonstrated that the GHR gene was under‐expressed in esophageal cancer tissues (p = 0.017). Conclusion The gene GHR and PLCE1 polymorphisms are associated with EC in the general population and the results need to be verified in future.
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Affiliation(s)
- Rong Wang
- Medical college, Qinghai University, Xining, Qinghai Province, China
| | - Lining Si
- Department of Critical-Care Medicine, Affiliated Hospital of Qinghai University, Xining, Qinghai Province, China
| | - Derui Zhu
- Medical college, Qinghai University, Xining, Qinghai Province, China
| | - Guoping Shen
- Medical college, Qinghai University, Xining, Qinghai Province, China
| | - Qifu Long
- Medical college, Qinghai University, Xining, Qinghai Province, China
| | - Yanli Zhao
- Medical college, Qinghai University, Xining, Qinghai Province, China
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