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Kong K, Ding X, Wang Y, Xu S, Li G, Wang X, Zhang M, Ni Y, Xu G. Circular RNA expression profile and functional analysis of circUvrag in light-induced photoreceptor degeneration. Clin Exp Ophthalmol 2024; 52:558-575. [PMID: 38282307 DOI: 10.1111/ceo.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 11/18/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Circular RNAs (circRNAs) are implicated in retinal pathophysiology; however, their expression profiles and functions in photoreceptor apoptosis are largely unknown. We explored circRNA-expression profiles and circUvrag (host gene: Uvrag, ultraviolet radiation resistance associated gene) function in light-induced photoreceptor apoptosis. METHODS Sprague-Dawley rats and 661 W photoreceptor cells were exposed to blue light to establish light-induced photoreceptor degeneration. Differentially expressed circRNAs were identified using microarrays. Potential functions of dysregulated circRNAs were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. CircUvrag expression and localization were evaluated using quantitative RT-PCR and fluorescence in situ hybridization, respectively. CircUvrag overexpression and knockdown were induced using a plasmid and a small interfering RNA, respectively, and retinal function and structure were assessed using scotopic electroretinography, haematoxylin-eosin staining, and TUNEL staining. Microglial migration was assessed using IBA1 immunostaining. The apoptosis ratio of photoreceptor cells in vitro was detected using flow cytometry. RESULTS We identified 764 differentially expressed circRNAs, which were potentially related with the development of retinal structures, including neurons, dendrites, and synapses, and might participate in nervous-system pathophysiology. Light exposure enriched circUvrag in the cytoplasm of photoreceptors in the outer nuclear layer (ONL). CircUvrag knockdown decreased photoreceptor apoptosis and microglial migration to the ONL after light exposure, preserving ONL thickness and a-wave amplitude. In vitro, circUvrag knockdown inhibited photoreceptor apoptosis, although circUvrag overexpression slightly promoted photoreceptor apoptosis. CONCLUSIONS CircUvrag knockdown attenuated light-induced photoreceptor apoptosis, and might be a potential target in retinal degeneration.
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Affiliation(s)
- Kangjie Kong
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xinyi Ding
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingchao Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Sisi Xu
- Department of Ophthalmology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gang Li
- Research Center, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xin Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Meng Zhang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingqin Ni
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Gezhi Xu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
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Luo S, Hu Q, Jiang B, Zhang Z, Sun D. Bioinformatics analysis for constructing a cellular senescence-related age-related macular degeneration diagnostic model and identifying relevant disease subtypes to guide treatment. Aging (Albany NY) 2024; 16:8044-8069. [PMID: 38742956 PMCID: PMC11131993 DOI: 10.18632/aging.205804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Age-related macular degeneration (AMD) is a condition causing progressive central vision loss. Growing evidence suggests a link between cellular senescence and AMD. However, the exact mechanism by which cellular senescence leads to AMD remains unclear. Employing machine learning, we established an AMD diagnostic model. Through unsupervised clustering, two distinct AMD subtypes were identified. GO, KEGG, and GSVA analyses explored the diverse biological functions associated with the two subtypes. By WGCNA, we constructed a coexpression network of differential genes between the subtypes, revealing the regulatory role of hub genes at the level of transcription factors and miRNAs. We identified 5 genes associated with inflammation for the construction of the AMD diagnostic model. Additionally, we observed that the level of cellular senescence and pathways related to programmed cell death (PCD), such as ferroptosis, necroptosis, and pyroptosis, exhibited higher expression levels in subtype B than A. Immune microenvironments also differed between the subtypes, indicating potentially distinct pathogenic mechanisms and therapeutic targets. In summary, by leveraging cellular senescence-associated gene expression, we developed an AMD diagnostic model. Furthermore, we identified two subtypes with varying expression patterns of senescence genes, revealing their differential roles in programmed cell death, disease progression, and immune microenvironments within AMD.
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Affiliation(s)
- Shan Luo
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Qiang Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Jiang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zhongyu Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Dawei Sun
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Jiang J, Wang S, Li Y, Wang Y, Liao R. Has-miR-199a-3p/RELA/SCD inhibits immune checkpoints in AMD and promotes macrophage-mediated inflammation and pathological angiogenesis through lipid metabolism pathway: A computational analysis. PLoS One 2024; 19:e0297849. [PMID: 38625951 PMCID: PMC11020405 DOI: 10.1371/journal.pone.0297849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/10/2024] [Indexed: 04/18/2024] Open
Abstract
More and more evidence shows that abnormal lipid metabolism leads to immune system dysfunction in AMD and promotes the occurrence of AMD by changing the homeostasis of ocular inflammation. However, the molecular mechanism underlying the effect of lipid metabolism on the phenotype and function of macrophages is still unclear, and the mechanism of association between AMD and cancer and COVID-19 has not been reported. The purpose of this study is to explore the interaction between lipid metabolism related genes, ferroptosis related genes and immunity in AMD, find out the key genes that affect the ferroptosis of AMD through lipid metabolism pathway and the molecular mechanism that mediates the action of macrophages, and find out the possible mechanism of lipid metabolism and potential co-therapeutic targets between AMD and cancer and COVID-19, so as to improve treatment decision-making and clinical results. For the first time, we have comprehensively analyzed the fatty acid molecule related genes, ferroptosis related genes and immune microenvironment of AMD patients, and determined that mast cells and M1 macrophages are the main causes of AMD inflammation, and found that SCD is the core gene in AMD that inhibits ferroptosis through lipid metabolism pathway, and verified the difference in the expression of SCD in AMD in a separate external data set. Based on the analysis of the mechanism of action of the SCD gene, we found for the first time that Has-miR-199a-3p/RELA/SCD is the core axis of action of lipid metabolism pathway to inhibit the ferroptosis of AMD. By inhibiting the immune checkpoint, we can enhance the immune cell activity of AMD and lead to the transformation of macrophages from M2 to M1, thereby promoting the inflammation and pathological angiogenesis of AMD. At the same time, we found that ACOX2 and PECR, as genes for fatty acid metabolism, may regulate the expression of SCD during the occurrence and development of COVID-19, thus affecting the occurrence and development of AMD. We found that FASD1 may be a key gene for the joint action of AMD and COVID-19, and SCD regulates the immune infiltration of macrophages in glioma and germ line tumors. In conclusion, our results can provide theoretical basis for the pathogenesis of AMD, help guide the treatment of AMD patients and their potentially related diseases and help to design effective drug targets.
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Affiliation(s)
- Jiang Jiang
- Department of Ophthalmology, The First Affiliated Hospital of Anhui Medical University, Anhui, China
- Department of Ophthalmology, The Third Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Shu Wang
- Department of Geriatrics, The Third Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Yun Li
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
- Kindstar Global Precision Medicine Institute, Wuhan, China
| | - Yi Wang
- Department of Oncology, The Third Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Rongfeng Liao
- Department of Ophthalmology, The First Affiliated Hospital of Anhui Medical University, Anhui, China
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Ren H, Lv W, Shang Z, Li L, Shen Q, Li S, Song Z, Cheng X, Meng X, Chen R, Zhang R. Identifying functional subtypes of IgA nephropathy based on three machine learning algorithms and WGCNA. BMC Med Genomics 2024; 17:61. [PMID: 38395835 PMCID: PMC10893719 DOI: 10.1186/s12920-023-01702-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/14/2023] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is one of the most common primary glomerulonephritis, which is a significant cause of renal failure. At present, the classification of IgAN is often limited to pathology, and its molecular mechanism has not been established. Therefore we aim to identify subtypes of IgAN at the molecular level and explore the heterogeneity of subtypes in terms of immune cell infiltration, functional level. METHODS Two microarray datasets (GSE116626 and GSE115857) were downloaded from GEO. Differential expression genes (DEGs) for IgAN were screened with limma. Three unsupervised clustering algorithms (hclust, PAM, and ConsensusClusterPlus) were combined to develop a single-sample subtype random forest classifier (SSRC). Functional subtypes of IgAN were defined based on functional analysis and current IgAN findings. Then the correlation between IgAN subtypes and clinical features such as eGFR and proteinuria was evaluated by using Pearson method. Subsequently, subtype heterogeneity was verified by subtype-specific modules identification based on weighted gene co-expression network analysis(WGCNA) and immune cell infiltration analysis based on CIBERSORT algorithm. RESULTS We identified 102 DEGs as marker genes for IgAN and three functional subtypes namely: viral-hormonal, bacterial-immune and mixed type. We screened seventeen genes specific to viral hormonal type (ATF3, JUN and FOS etc.), and seven genes specific to bacterial immune type (LIF, C19orf51 and SLPI etc.). The subtype-specific genes showed significantly high correlation with proteinuria and eGFR. The WGCNA modules were in keeping with functions of the IgAN subtypes where the MEcyan module was specific to the viral-hormonal type and the MElightgreen module was specific to the bacterial-immune type. The results of immune cell infiltration revealed subtype-specific cell heterogeneity which included significant differences in T follicular helper cells, resting NK cells between viral-hormone type and control group; significant differences in eosinophils, monocytes, macrophages, mast cells and other cells between bacterial-immune type and control. CONCLUSION In this study, we identified three functional subtypes of IgAN for the first time and specific expressed genes for each subtype. Then we constructed a subtype classifier and classify IgAN patients into specific subtypes, which may be benefit for the precise treatment of IgAN patients in future.
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Affiliation(s)
- Hongbiao Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Liangshuang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Qi Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Xiangshu Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Xin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Rui Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China.
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Zhang W, He Y, Zhang Y. CircRNA in ocular neovascular diseases: Fundamental mechanism and clinical potential. Pharmacol Res 2023; 197:106946. [PMID: 37797661 DOI: 10.1016/j.phrs.2023.106946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Ocular neovascular disease (OND), characterized by the aberrant formation of immature blood vessels, is the leading cause of vision impairment and blindness. It is important to find effective ways to diagnose and treat these diseases. Circular RNA (circRNA) is a group of endogenous non-coding RNA that play a crucial role in regulating different biological processes. Due to their close association with ocular disease and angiogenesis, circRNAs have become a hotspot in OND research. In this review, we intensively investigate the possibility of using circRNAs in the management of ONDs. In general, angiogenesis is divided into five phases. On the basis of these five steps, we describe the potential of using circRNAs by introducing how they regulate angiogenesis. Subsequently, the interactions between circRNAs and ONDs, including pterygium, corneal neovascularization, age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity, are analyzed in detail. We also introduce the potential use of circRNAs as OND diagnostic biomarkers. Finally, we summarize the prospects of using circRNAs as a potential strategy in OND management. The gaps in recent research are also pointed out with the purpose of promoting the introduction of circRNAs into clinical applications.
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Affiliation(s)
- Wenxin Zhang
- Department of Ophthalmology, 2nd Hospital of Jilin University, Changchun 130041, Jilin, China
| | - Yuxi He
- Department of Ophthalmology, 2nd Hospital of Jilin University, Changchun 130041, Jilin, China
| | - Yan Zhang
- Department of Ophthalmology, 2nd Hospital of Jilin University, Changchun 130041, Jilin, China; Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China.
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Zhang R, Tao Y, Huang J. The Application of MicroRNAs in Glaucoma Research: A Bibliometric and Visualized Analysis. Int J Mol Sci 2023; 24:15377. [PMID: 37895056 PMCID: PMC10607922 DOI: 10.3390/ijms242015377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Glaucoma is similar to a neurodegenerative disorder and leads to global irreversible loss of vision. Despite extensive research, the pathophysiological mechanisms of glaucoma remain unclear, and no complete cure has yet been identified for glaucoma. Recent studies have shown that microRNAs can serve as diagnostic biomarkers or therapeutic targets for glaucoma; however, there are few bibliometric studies that focus on using microRNAs in glaucoma research. Here, we have adopted a bibliometric analysis in the field of microRNAs in glaucoma research to manifest the current tendencies and research hotspots and to present a visual map of the past and emerging tendencies in this field. In this study, we retrieved publications in the Web of Science database that centered on this field between 2007 and 2022. Next, we used VOSviewer, CiteSpace, Scimago Graphica, and Microsoft Excel to present visual representations of a co-occurrence analysis, co-citation analysis, tendencies, hotspots, and the contributions of authors, institutions, journals, and countries/regions. The United States was the main contributor. Investigative Ophthalmology and Visual Science has published the most articles in this field. Over the past 15 years, there has been exponential growth in the number of publications and citations in this field across various countries, organizations, and authors. Thus, this study illustrates the current trends, hotspots, and emerging frontiers and provides new insight and guidance for searching for new diagnostic biomarkers and clinical trials for glaucoma in the future. Furthermore, international collaborations can also be used to broaden and deepen the field of microRNAs in glaucoma research.
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Affiliation(s)
| | | | - Jufang Huang
- Department of Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (R.Z.); (Y.T.)
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Ayaz H, Aslam N, Awan FM, Basri R, Rauff B, Alzahrani B, Arif M, Ikram A, Obaid A, Naz A, Khan SN, Yang BB, Nazir A. Mapping CircRNA-miRNA-mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection. PLoS One 2023; 18:e0283589. [PMID: 37053191 PMCID: PMC10101458 DOI: 10.1371/journal.pone.0283589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/11/2023] [Indexed: 04/14/2023] Open
Abstract
Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection.
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Affiliation(s)
- Hassan Ayaz
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Nouman Aslam
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Rabea Basri
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Bisma Rauff
- Department of Biomedical Engineering, University of Engineering and Technology (UET), Lahore, Narowal, Pakistan
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Muhammad Arif
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Aqsa Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Ayesha Obaid
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Burton B Yang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
| | - Azhar Nazir
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Khyber Pakhtunkhwa, Pakistan
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Zhu B, Gao J, Zhang Y, Liao B, Zhu S, Li C, Liao J, Liu J, Jiang C, Zeng J. CircRNA/miRNA/mRNA axis participates in the progression of partial bladder outlet obstruction. BMC Urol 2022; 22:191. [PMID: 36434693 PMCID: PMC9700926 DOI: 10.1186/s12894-022-01132-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND More and more evidence showed that circRNA/miRNA/mRNA axis played a vital role in the pathogenesis of some diseases. However, the role of circRNA/miRNA/mRNA axis in partial bladder outlet obstruction (pBOO) remains unknown. Our study aimed to explore the complex regulatory mechanism of circRNA/miRNA/mRNA axis in pBOO. METHODS The pBOO rat model was established, and the bladder tissues were collected for mRNA sequencing. The differentially expressed mRNAs were analyzed by high-throughput sequencing, and the GO and KEGG analysis of the differentially expressed mRNAs were performed. Competing endogenous RNAs (ceRNAs) analysis identified the potential regulation function of circRNA/miRNA/mRNA axis in pBOO. qRT-PCR detected the expression of circRNA/miRNA/mRNA. miRanda software was performed to predict the relationship between circRNA and miRNA, miRNA and mRNA. RESULTS Compared with the sham group, a total of 571 mRNAs were differentially expressed in the pBOO group, of which 286 were up-regulated and 285 were down-regulated. GO analysis showed that the mRNAs were mainly involved in cellular process, single-organism process, and cell, etc. KEGG analysis showed that the enriched signaling pathways were metabolic pathways, cell adhesion molecules (CAMs), and HTLV-I infection, etc. Based on the previous transcriptome data and differentially expressed circRNAs, we drew the ceRNA network regulation diagram. qRT-PCR results confirmed that chr3:113195876|113197193/rno-miR-30c-1-3p/Gata4, chr1:126188351|126195625/rno-miR-153-5p/Diaph3, and chr9:81258380|81275269/rno-miR-135b-5p/Pigr axis may have ceRNA function. miRanda confirmed there have the binding sites of circRNA/miRNA/mRNA axis. CONCLUSIONS CircRNA/miRNA/mRNA axis was involved in the progression of pBOO. Our research on the circRNA/miRNA/mRNA axis revealed new pathogenesis and treatment strategies for pBOO.
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Affiliation(s)
- Baoyi Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jun Gao
- grid.410737.60000 0000 8653 1072Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, 511518 Guangdong People’s Republic of China
| | - Yuying Zhang
- Department of Child Health Care, Shenzhen Longhua Maternity and Child Health Care Hospital, Shenzhen, 518000 Guangdong People’s Republic of China
| | - Baojian Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China ,grid.9227.e0000000119573309Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510700 Guangdong People’s Republic of China
| | - Sihua Zhu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chunling Li
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Junhao Liao
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianjia Liu
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Chonghe Jiang
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
| | - Jianwen Zeng
- grid.410737.60000 0000 8653 1072Department of Urology, The Sixth Affiliated Hospital of Guangzhou Medical University (Qingyuan People’s Hospital), B24 Yinquan Road, Qingcheng, Qingyuan, 511500 Guangdong People’s Republic of China
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Li H, Ye Z, Li Z. Identification of the potential biological target molecules related to primary open-angle glaucoma. BMC Ophthalmol 2022; 22:188. [PMID: 35461232 PMCID: PMC9034601 DOI: 10.1186/s12886-022-02368-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 03/21/2022] [Indexed: 12/31/2022] Open
Abstract
Background To identify the potential biological target molecules and the corresponding interaction networks in primary open-angle glaucoma (POAG) development. Methods The microarray datasets of GSE138125 and GSE27276 concerning lncRNA and mRNA expression profiles in trabecular meshwork of POAG were downloaded from the Gene Expression Omnibus database. The R software was applied to identify differentially expressed (DE) lncRNAs and mRNAs in POAG, and to perform GO and KEGG functional enrichment analysis. Protein–protein interaction (PPI) network and module analysis, and lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) network were performed by Cytoscape software. Results A total of 567 DE-mRNAs were identified from GSE138125 and GSE27276, including 298 up-regulated and 269 down-regulated mRNAs, which were found enriching in biological processes of extracellular matrix organization and epidermis development, respectively. KEGG pathway enrichment analysis further revealed that module genes in PPI network were primarily involved in the AGE-PAGE, PI3K-Akt and TGF-β signaling pathways. Moreover, 897 up-regulated and 1036 down-regulated DE-lncRNAs were identified from GSE138125. Through literature review and databases searching, we obtained 712 lncRNA-miRNA and 337 miRNA-mRNA pairs based on the selected eight POAG-related miRNAs. After excluding 702 lncRNAs and 284 mRNAs that were not comprised in the DE-lncRNA and DE-mRNAs, a total of 53 lncRNA nodes, eight miRNA nodes, 10 mRNA nodes, and 78 edges were included in the final ceRNA network. Conclusions This study demonstrated the lncRNA and mRNA expression profiles of trabecular meshwork in POAG patients and the normal controls, and identified potentially ceRNAs and pathways which might improve the pathogenic understanding of this ocular disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-022-02368-0.
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Affiliation(s)
- Hongyu Li
- Medical School of Chinese PLA, Beijing, China.,Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China
| | - Zi Ye
- Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China.
| | - Zhaohui Li
- Medical School of Chinese PLA, Beijing, China. .,Senior Department of Ophthalmology, the Third Medical Center of PLA General Hospital, Beijing, China.
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Li Y, Liu X, Zhang W, Song X, Zhang L, Xiao C. Differently Expressed Circular RNAs in Lacrimal Sacs From Patients With Chronic Dacryocystitis. Front Genet 2022; 13:834111. [PMID: 35295950 PMCID: PMC8918544 DOI: 10.3389/fgene.2022.834111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
This study was designed to identify differently expressed circular RNAs (circRNAs) and investigate their potential roles in lacrimal sacs from patients with chronic dacryocystitis. The lacrimal sac samples of three chronic dacryocystitis patients and three control subjects were collected for RNA sequencing after ribosomal RNA was depleted. Differently expressed circRNAs and messenger RNAs (mRNAs) were used for co-expression analysis. CircRNA-microRNA (miRNA)-mRNA interaction network were also established by miRanda software. Meanwhile, pathway and functional enrichment analysis were conducted for the down- and up-regulated mRNAs in the circRNA-mRNA co-expression network. The expression levels of circRNAs and mRNAs in chronic dacryocystitis and control samples were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). In all the 3,909 circRNAs predicted through RNA sequencing, 25 circRNAs (20 up-regulated and 5 down-regulated) expressed differently in chronic dacryocystitis samples. Besides, there identified 1,486 differentially expressed mRNAs. Of these differently expressed circRNAs and mRNAs, eight were validated by qRT-PCR, including MYH2, DSP, CD27, CCL5, FN1, has_circ_0004792, has_circ_0001062, and has_circ_0115476. Gene Ontology (GO) analysis indicated that the majority of altered mRNAs in this co-expression network were involved in immune system processes and meanwhile Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these altered expressed mRNAs were also amplified in bacterial invasion of epithelial cells, both of which were thought to be involved in the pathogenesis of chronic dacryocystitis. In the circRNA-miRNA-mRNA interaction network, six circRNAs were found to be related to Th1 and Th2 cell differentiation, which was closely associated with the development of chronic dacryocystitis. This study identified statistically significant differences between circRNAs and mRNAs of lacrimal sac samples of chronic dacryocystitis patients and control individuals and provides novel insight into the regulatory mechanism of circRNAs, miRNAs, and mRNAs in the pathogenesis of chronic dacryocystitis.
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Affiliation(s)
- Yue Li
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xueru Liu
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Wenyue Zhang
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xuefei Song
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Leilei Zhang
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- *Correspondence: Leilei Zhang, ; Caiwen Xiao,
| | - Caiwen Xiao
- Department of Ophthalmology, School of Medicine, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- *Correspondence: Leilei Zhang, ; Caiwen Xiao,
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11
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Sun Z, Song L, Li J. Knockdown of small nucleolar RNA host gene 10 (SNHG10) alleviates the injury of human neuroblastoma cells via the miR-1277-5p/insulin substrate receptor 2 axis. Bioengineered 2022; 13:709-720. [PMID: 34967697 PMCID: PMC8805890 DOI: 10.1080/21655979.2021.2012623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/25/2021] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease is a common neurodegenerative disease with a complex physio-pathology. So far, there is no effective medical strategies to prevent the progression of Parkinson's disease. Understanding the mechanisms underlying the progression of Parkinson's disease could provide insights into the formulation of novel preventative or treatment strategies. Small nucleolar RNA host gene 10 (SNHG10) is a lncRNA which has been implicated in the development of many cancers. However, its potential role in Parkinson's disease remains unknown. In this study, we found that SNHG10 was upregulated while miR-1277-5p was downregulated in the Parkinson's disease cell model of 1-Methyl-4-phenyl-pyridine ion (MPP+) induced SH-SY5Y cells. We further revealed that SNHG10 sponged miR-1277-5p to negatively regulate its expression, and miR-1277-5p could bind to the 3'UTR of insulin substrate receptor 2 (IRS2) mRNA to suppress its expression. These data suggest that SNHG10 regulates IRS2 through interacting with miR-1277-5p in the cell model of Parkinson's disease. Through a series of molecular experiments and functional assays, we demonstrated that downregulating SNHG10 in the cell model of Parkinson's disease attenuated the cell injury by reducing the expression of IRS2. Meanwhile, inhibiting miR-1277-5p or overexpressing IRS2 could partially reverse the effect of SNHG10 knockdown. In summary, our data indicate that knockdown of SNHG10 mitigates MPP+ induced damage in SH-SY5Y cells via the miR-1277-5p/IRS2 axis.
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Affiliation(s)
- Zhaoming Sun
- Department of Neurology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
| | - Lixiang Song
- Department of Neurology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
| | - Jiazhen Li
- Department of Neurology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China
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12
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Zhang D, Zhang G, Yu K, Zhang X, Jiang A. Circ_0003204 knockdown protects endothelial cells against oxidized low-density lipoprotein-induced injuries by targeting the miR-491-5p-ICAM1 pathway. J Thromb Thrombolysis 2021; 53:302-312. [PMID: 34797473 DOI: 10.1007/s11239-021-02606-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 11/30/2022]
Abstract
Emerging evidence indicates that circular RNA (circRNA) is implicated in the development of atherosclerosis (AS). This study investigated the effect of circ_0003204 on endothelial cell function and explored the functional mechanism of circ_0003204 in AS progression. AS cell models were constructed by treating human umbilical vein endothelial cells (HUVEC) with oxidized low-density lipoprotein (ox-LDL). The expression of circ_0003204 was detected by quantitative real-time PCR (qPCR). The releases of pro-inflammatory factors were determined by ELISA. Cell viability was checked by CCK-8 assay. Cell apoptosis was monitored by flow cytometry assay. The ability of angiogenesis was assessed by tube formation assay. The protein levels of cell development- and apoptosis-related markers were measured by western blot. The binding relationship between miR-491-5p and circ_0003204 or intercellular adhesion molecule 1 (ICAM1) was verified by dual-luciferase reporter assay or RIP assay. The expression of circ_0003204 was strengthened in ox-LDL-treated HUVECs. Circ_0003204 knockdown inhibited ox-LDL-induced inflammation and cell apoptosis, and promoted ox-LDL-depleted cell viability and tube formation ability in HUVECs. MiR-491-5p was a target of circ_0003204, and miR-491-5p directly bound to ICAM1 3'UTR. Accordingly, circ_0003204 positively regulated ICAM1 expression by targeting miR-491-5p. Rescue experiments presented that miR-491-5p inhibition reversed the effects of circ_0003204 knockdown, and ICAM1 overexpression abolished the effects of miR-491-5p restoration. Circ_0003204 knockdown protects HUVECs against ox-LDL-induced injuries by targeting the miR-491-5p-ICAM1 pathway, hinting that circ_0003204 inhibition might prevent AS development.
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Affiliation(s)
- Dongying Zhang
- Department of Cardiology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University,, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, China
| | - Gang Zhang
- Department of Cardiology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University,, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, China
| | - Kun Yu
- Department of Cardiology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University,, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, China
| | - Xiwen Zhang
- Department of Cardiology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University,, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, China
| | - Aixia Jiang
- Department of Cardiology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University,, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, China.
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13
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ElShelmani H, Brennan I, Kelly DJ, Keegan D. Differential Circulating MicroRNA Expression in Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms222212321. [PMID: 34830203 PMCID: PMC8625913 DOI: 10.3390/ijms222212321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023] Open
Abstract
This study explored the expression of several miRNAs reported to be deregulated in age-related macular degeneration (AMD). Total RNA was isolated from sera from patients with dry AMD (n = 12), wet AMD (n = 14), and controls (n = 10). Forty-two previously investigated miRNAs were selected based on published data and their role in AMD pathogenesis, such as angiogenic and inflammatory effects, and were co-analysed using a miRCURY LNA miRNA SYBR® Green PCR kit via quantitative real-time polymerase chain reaction (qRT-PCR) to validate their presence. Unsupervised hierarchical clustering indicated that AMD serum specimens have a different miRNA profile to healthy controls. We successfully validated the differentially regulated miRNAs in serum from AMD patients versus controls. Eight miRNAs (hsa-let-7a-5p, hsa-let-7d-5p, hsa-miR-23a-3p, hsa-miR-301a-3p, hsa-miR-361-5p, hsa-miR-27b-3p, hsa-miR-874-3p, hsa-miR-19b-1-5p) showed higher expression in the serum of dry AMD patients than wet AMD patients and compared with healthy controls. Increased quantities of certain miRNAs in the serum of AMD patients indicate that these miRNAs could potentially serve as diagnostic AMD biomarkers and might be used as future AMD treatment targets. The discovery of significant serum miRNA biomarkers in AMD patients would provide an easy screening tool for at-risk populations.
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Affiliation(s)
- Hanan ElShelmani
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
| | - Ian Brennan
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
- University College Cork, College Road, Cork, Ireland
| | - David J. Kelly
- Zoology Department, School of Natural Sciences, Trinity College Dublin, University of Dublin, Dublin 2, Ireland;
| | - David Keegan
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
- Correspondence:
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MicroRNA-27a Promotes Oxidative-Induced RPE Cell Death through Targeting FOXO1. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6666506. [PMID: 34761005 PMCID: PMC8575620 DOI: 10.1155/2021/6666506] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/21/2022]
Abstract
Age-related macular degeneration (AMD) is a multifactor disease, which is primarily characterized by retinal pigment epithelium (RPE) cell loss. Since the retina is the most metabolically active tissue, RPE cells are exposed to consistent oxidative environment. So, oxidation-induced RPE cell death has long been considered a contributor to the onset of AMD. Here, we applied a retinal degeneration (RD) rat model induced by blue light-emitting diode (LED) and a cell model constructed by H2O2 stimulus to mimic the prooxidant environment of the retina. We detected that the expression of miR-27a was upregulated and the expression of FOXO1 was downregulated in both models. So, we furtherly investigated the role of miR-27a-FOXO1 axis in RPE in protesting against oxidants. Lentivirus-mediated RNA was injected intravitreally into rats to modulate the miR-27a-FOXO1 axis. Retinal function and histopathological changes were evaluated by electroretinography (ERG) analysis and hematoxylin and eosin (H&E) staining, respectively. Massive photoreceptor and RPE cell death were examined by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL). The damage to the retina was aggravated in the FOXO1 gene-knockdown and miR-27a-overexpression groups after exposure to LED but was alleviated in the FOXO1 gene-overexpression or miR-27a-knockdown groups. Dual luciferase assay was used to detect the binding site of miR-27a and FOXO1. Upregulated miR-27a inhibited the expression of FOXO1 by directly binding to the FOXO1 mRNA 3′UTR and decreased the autophagy activity of ARPE-19 cells, resulting in the accumulation of reactive oxygen species (ROS) and decrease of cell viability. The results suggest that miR-27a is a negative regulator of FOXO1. Also, our data emphasize the prominent role of miR-27a/FOXO1 axis in modulating ROS accumulation and cell death in RPE cell model under oxidative stress and influencing the retinal function in the LED-induced RD rat model.
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15
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Investigation of Key Signaling Pathways Associating miR-204 and Common Retinopathies. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568113. [PMID: 34646884 PMCID: PMC8505061 DOI: 10.1155/2021/5568113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/15/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
MicroRNAs are a large group of small noncoding RNAs that work in multiple cellular pathways. miR-204, as one of the key axes in the development, maintenance, and pathogenesis of the retina, plays several roles by modulating its target genes. This study was aimed at evaluating the target genes of miR-204 involved in the development and progression of common retinopathies such as glaucoma, retinoblastoma, and age-related macular degeneration. In this study, three datasets related to retinopathies (GSE50195, GSE27276, and GSE97508) were selected from Gene Expression Omnibus. miR-204 target genes were isolated from TargeScan. The shares between retinopathy and miR-204 target genes were then categorized. Using Enrichr and STRING, we highlighted the signaling pathways and the relationships between the proteins. SHC1 events in ERBB2, adherent junction's interactions, NGF signaling via TRKA from the plasma membrane, IRF3-mediated activation of type 1 IFN, pathways in upregulated genes and G0 and early G1, RORA-activated gene expression, PERK-regulated gene expression, adherent junction's interactions, and CREB phosphorylation pathways in downregulated genes were identified in glaucoma, retinoblastoma, and age-related macular degeneration. WEE1, SMC2, HMGB1, RRM2, and POLA1 proteins were also observed to be involved in the progression and invasion of retinoblastoma; SLC24A2 and DTX4 in age-related macular degeneration; and EPHB6, EFNB3, and SHC1 in glaucoma. Continuous bioinformatics analysis has shown that miR-204 has a significant presence and expression in retinal tissue, and approximately 293 genes are controlled and regulated by miR-204 in this tissue; also, target genes of miR-204 have the potential to develop various retinopathies; thus, a study of related target genes can provide appropriate treatment strategies in the future.
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