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Nowak-Malczewska DM, Swierkowska J, Gajecka M. Differentially expressed microRNAs targeting genes in key pathways in keratoconus. Front Genet 2024; 15:1301676. [PMID: 38469119 PMCID: PMC10925626 DOI: 10.3389/fgene.2024.1301676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction: Keratoconus (KTCN) is a corneal ectasia, characterized by a progressive thinning and protrusion of the cornea, with a complex etiology involving genetic, behavioral, lifestyle, and environmental factors. Previous studies indicated that microRNAs (miRNAs) could be involved in KTCN pathogenesis. This in silico study aimed to identify precursor microRNAs (pre-miRNAs) differentially expressed in KTCN corneas and to characterize mature miRNAs and their target genes. Materials and methods: Expression levels of pre-miRNAs were retrieved from our previously obtained RNA sequencing data of 25 KTCN and 25 non-KTCN human corneas (PMID:28145428, PMID:30994860). Differential expression with FDR ≤0.01 and ≥1.5-fold changes were considered significant. Lists of target genes (target score ≥90) of mature miRNAs were obtained from miRDB. Revealed up-/downregulated miRNAs and their target genes were assessed in databases and literature. Enrichment analyses were completed applying the DAVID database. Results: From a total of 47 pre-miRNAs, six were remarkably upregulated (MIR184, MIR548I1, MIR200A, MIR6728, MIR429, MIR1299) and four downregulated (MIR6081, MIR27B, MIR23B, MIR23A) in KTCN corneas. Out of the 1,409 target genes, 220 genes with decreased and 57 genes with increased expression levels in KTCN samples vs non-KTCN samples were found. The extracellular matrix (ECM) organization, response to mechanical stimulus, regulation of cell shape, and signal transduction processes/pathways were identified as distinctive in enrichment analyses. Also, processes associated with the regulation of transcription and DNA binding were listed. Conclusion: Indicated miRNAs and their target genes might be involved in KTCN pathogenesis via disruption of crucial molecular processes, including ECM organization and signal transduction.
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Affiliation(s)
- Dorota M. Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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Hong Y, Wu J, Sun Y, Zhang S, Lu Y, Ji Y. ceRNA network construction and identification of hub genes as novel therapeutic targets for age-related cataracts using bioinformatics. PeerJ 2023; 11:e15054. [PMID: 36987450 PMCID: PMC10040182 DOI: 10.7717/peerj.15054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/21/2023] [Indexed: 03/30/2023] Open
Abstract
Background The aim of this study is to investigate the genetic and epigenetic mechanisms involved in the pathogenesis of age-related cataract (ARC). Methods We obtained the transcriptome datafile of th ree ARC samples and three healthy, age-matched samples and used differential expression analyses to identify the differentially expressed genes (DEGs). The differential lncRNA-associated competing endogenous (ceRNA) network, and the protein-protein network (PPI) were constructed using Cytoscape and STRING. Cluster analyses were performed to identify the underlying molecular mechanisms of the hub genes affecting ARC progression. To verify the immune status of the ARC patients, immune-associated analyses were also conducted. Results The PPI network identified the FOXO1 gene as the hub gene with the highest score, as calculated by the Maximal Clique Centrality (MCC) algorithm. The ceRNA network identified lncRNAs H19, XIST, TTTY14, and MEG3 and hub genes FOXO1, NOTCH3, CDK6, SPRY2, and CA2 as playing key roles in regulating the pathogenesis of ARC. Additionally, the identified hub genes showed no significant correlation with an immune response but were highly correlated with cell metabolism, including cysteine, methionine, and galactose. Discussion The findings of this study may provide clues toward ARC pathogenic mechanisms and may be of significance for future therapeutic research.
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Affiliation(s)
- Yingying Hong
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Jiawen Wu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Yang Sun
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Shenghai Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Yi Lu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Yinghong Ji
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
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Chen S, Zhang C, Shen L, Hu J, Chen X, Yu Y. Noncoding RNAs in cataract formation: star molecules emerge in an endless stream. Pharmacol Res 2022; 184:106417. [PMID: 36038044 DOI: 10.1016/j.phrs.2022.106417] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
For decades, research on the pathological mechanism of cataracts has usually focused on the abnormal protein changes caused by a series of risk factors. However, an entire class of molecules, termed non-coding RNA (ncRNA), was discovered in recent years and proven to be heavily involved in cataract formation. Recent studies have recognized the key regulatory roles of ncRNAs in cataracts by shaping cellular activities such as proliferation, apoptosis, migration and epithelial-mesenchymal transition (EMT). This review summarizes our current insight into the biogenesis, properties and functions of ncRNAs and then discusses the development of research on ncRNAs in cataracts. Considering the significant role of ncRNA in cataract formation, research on novel associated regulatory mechanisms is urgently needed, and the development of therapeutic alternatives for the treatment of cataracts seems promising.
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Affiliation(s)
- Silong Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Chengshou Zhang
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Lifang Shen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China
| | - Jianghua Hu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Department of Ophthalmology, Jiande Branch, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangjun Chen
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China; Institute of Translational Medicine, Zhejiang University School of Medicine, 268 Kaixuan Road, China.
| | - Yibo Yu
- Eye Center of the Second Affiliated Hospital, Medical College of Zhejiang University, 88 Jiefang Road, Hangzhou, China.
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Liu Y, Li S, Liu Y, Lv X, Zhou Q. MicroRNA-124 facilitates lens epithelial cell apoptosis by inhibiting SPRY2 and MMP-2. Mol Med Rep 2021; 23:381. [PMID: 33760112 PMCID: PMC7986009 DOI: 10.3892/mmr.2021.12020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022] Open
Abstract
Age-related cataract (ARC) is the primary cause of blindness worldwide. Abnormal expression of microRNAs (miRNAs/miRs) has been reported to be associated with multiple diseases, including ARC. However, the potential role of miR-124 in ARC remains unclear. The present study used the human lens epithelial cell line, SRA01/04, to investigate the potential role of miR-124 in ARC. Reverse transcription-quantitative PCR analysis was performed to detect the expression levels of miR-124, protein sprouty homolog 2 (SPRY2) and matrix metalloproteinase-2 (MMP-2) in ARC tissues, while western blotting was performed to detect the protein levels of SPRY2 and MMP-2. Cell viability and apoptosis of SRA01/04 cells were assessed via Cell Counting Kit-8 and TUNEL assays, respectively. The interaction between miR-124 and SPRY2 or MMP-2 was confirmed via the dual-luciferase reporter and RNA immunoprecipitation assays. The results of the present study demonstrated that miR-124 expression was significantly upregulated in ARC tissues, and knockdown of miR-124 increased SRA01/04 cell viability and suppressed apoptosis. In addition, SPRY2 and MMP-2 expression was decreased in ARC tissues, and were demonstrated to directly bind to miR-124. Overexpression of SPRY2 or MMP-2 increased SRA01/04 cell viability and repressed apoptosis, the effects of which were reversed following overexpression of miR-124. Taken together, these results suggested that miR-124 facilitates lens epithelial cell apoptosis by modulating SPRY2 or MMP-2 expression, providing a novel treatment approach for ARC.
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Affiliation(s)
- Yan Liu
- Department of Ophthalmology, The First People's Hospital of Changzhou, Changzhou, Jiangsu 223000, P.R. China
| | - Shuting Li
- Department of Ophthalmology, The First People's Hospital of Changzhou, Changzhou, Jiangsu 223000, P.R. China
| | - Yao Liu
- Department of Ophthalmology, The First People's Hospital of Changzhou, Changzhou, Jiangsu 223000, P.R. China
| | - Xujing Lv
- Department of Ophthalmology, The First People's Hospital of Changzhou, Changzhou, Jiangsu 223000, P.R. China
| | - Qing Zhou
- Department of Third Institute of Clinical Medicine, Soochow University, Suzhou, Jiangsu 215006, P.R. China
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Liang S, Dou S, Li W, Huang Y. Profiling of circular RNAs in age-related cataract reveals circZNF292 as an antioxidant by sponging miR-23b-3p. Aging (Albany NY) 2020; 12:17271-17287. [PMID: 32913142 PMCID: PMC7521481 DOI: 10.18632/aging.103683] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
Age-related cataract (ARC) is one of the major causes of visual impairment and reversible blindness worldwide. Accumulating evidence has revealed that circular RNAs (circRNAs) are involved in multiple regulatory processes in various ocular diseases. However, the expression profile, regulatory roles, and underlying mechanisms of circRNAs in ARC remain largely unknown. Herein we deep-sequenced circRNAs of anterior lens capsules from normal and ARC lenses, and detected 23,787 candidate circRNAs. Of these, 466 were significantly differentially expressed, and a higher correlation in down-regulated circRNAs between ARC and diabetic cataract was observed compared with up-regulated ones. Subsequent bioinformatics analysis disclosed that certain differentially expressed circRNAs participated in oxidative stress and apoptosis-related signaling pathways in ARC. Notably, the level of circZNF292 was significantly decreased, while miR-23b-3p was significantly increased in ARC. The target region prediction and dual-luciferase reporter assays proved that circZNF292 acted as a competitive endogenous RNA to regulate the expression of anti-oxidative genes through competing with miR-23b-3p. Our results indicate that circZNF292, a down-regulated circRNA in the anterior lens capsule of ARC patients, may be involved in resistance to oxidative damage and apoptosis of lens epithelial cells by sponging miR-23b-3p, providing a potential target for prevention and treatment of ARC.
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Affiliation(s)
- Shuqi Liang
- Medical College of Qingdao University, Qingdao, China,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, China
| | - Shengqian Dou
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, China,Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
| | - Wenfeng Li
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yusen Huang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, China,Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China
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