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Zhu W, Chen Y, Xiao J, Cheng C, Ma G, Wang Y, Zhang Y, Chen M. Ferroptosis-Related Genes in IgA Nephropathy: Screening for Potential Targets of the Mechanism. Int J Genomics 2024; 2024:8851124. [PMID: 39171207 PMCID: PMC11338665 DOI: 10.1155/2024/8851124] [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: 05/16/2023] [Revised: 06/04/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Aims: Exploring key genes and potential molecular pathways of ferroptosis in immunoglobulin A nephropathy (IgAN). Methods: The IgAN datasets and ferroptosis-related genes (FRGs) were obtained in the Gene Expression Omnibus (GEO) and FerrDb database. Differentially expressed genes (DEGs) were identified using R software and intersected with FRGs to obtain differentially expressed FRGs (DE-FRGs). After that, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (PEA) and Gene Ontology (GO) functional annotation were performed on DE-FRGs. In the Search Tool for the Retrieval of Interacting Genes (STRING) website, we construct a protein-protein interaction (PPI) network. The PPI network was further investigated with screening hub genes with Cytoscape software. The core genes were then subjected to gene set enrichment analysis (GSEA). Finally, the samples were analyzed for immune infiltration in R, and the correlation between hub genes and immune cells was analyzed. Results: A total of 347 DEGs were identified. CD44, CDO1, CYBB, IL1B, RRM2, AKR1C1, activated transcription factor-3 (ATF3), CDKN1A, GDF15, JUN, MGST1, MIOX, MT1G, NR4A1, PDK4, TNFAIP3, and ZFP36 were determined as DE-FRGs. JUN, IL1B, and ATF3 were then screened as hub genes. GSEA and immune infiltration analysis revealed that the hub genes were closely associated with immune inflammatory responses such as NOD-like receptor signaling, IL-17 signaling, and TNF signaling. Conclusions: Our results show that JUN and ATF3 are possibly critical genes in the process of IgAN ferroptosis and may be related with immune cell infiltration.
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Affiliation(s)
- Wenhui Zhu
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
- College of Traditional Chinese MedicineChangchun University of Chinese Medicine, Changchun, China
| | - Yao Chen
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Jing Xiao
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Chuchu Cheng
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Guijie Ma
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Yang Wang
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
| | - Yonggang Zhang
- Department of Renal DivisionFirst People's Hospital of Qiqihar City, Qiqihar, China
| | - Ming Chen
- Department of Renal DivisionHeilongjiang Academy of Chinese Medicine Sciences, Harbin, China
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Che J, Yang X, Zhao X, Li Y, Jin Z, Xu C. Risk factor prediction and immune correlation analysis of cuproptosis-related gene in osteoarthritis. J Cell Mol Med 2024; 28:e18574. [PMID: 39087591 PMCID: PMC11292577 DOI: 10.1111/jcmm.18574] [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: 02/20/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Osteoarthritis (OA) is a widespread inflammatory joint disease with significant global disability burden. Cuproptosis, a newly identified mode of cell death, has emerged as a crucial factor in various pathological conditions, including OA. In this context, our study aims to investigate the intrinsic relationship between cuproptosis-related genes (CRGs) and OA, and assess their potential as biomarkers for OA diagnosis and treatment. Datasets from the GEO databases were analysed the differential expression of CRGs, leading to the identification of 10 key CRGs (CDKN2A, DLD, FDX1, GLS, LIAS, LIPT1, MTF1, PDHA1, DLAT and PDHB). A logistic regression analysis and calibration curves were used to show excellent diagnostic accuracy. Consensus clustering revealed two CRG patterns, with Cluster 1 indicating a closer association with OA progression. RT-PCR confirmed a significant increase in the expression levels of these nine key genes in IL-1β-induced C28/i2 cells, and the expression of CDKN2A and FDX1 were also elevated in conditioned monocytes, while the expression of GLS and MTF1 were significantly decreased. In vitro experiments demonstrated that the expression levels of these 7/10 CRGs were significantly increased in chondrocytes induced by IL-1β, and upon stimulation with cuproptosis inducers, chondrocyte apoptosis was exacerbated, accompanied by an increase in the expression of cuproptosis-related proteins. These further substantiated our research findings and indicated that the nine selected cuproptosis genes have high potential for application in the diagnosis of OA.
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Affiliation(s)
- Jingmin Che
- Shaanxi Provincial Key Laboratory of Infection and Immune DiseasesShaanxi Provincial People's HospitalXi'anShaanxiChina
- Shaanxi Engineering Research Center of Cell ImmunologyShaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Xiaoli Yang
- Shaanxi Provincial Key Laboratory of Infection and Immune DiseasesShaanxi Provincial People's HospitalXi'anShaanxiChina
- Shaanxi Engineering Research Center of Cell ImmunologyShaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Xiangrong Zhao
- Shaanxi Provincial Key Laboratory of Infection and Immune DiseasesShaanxi Provincial People's HospitalXi'anShaanxiChina
- Shaanxi Engineering Research Center of Cell ImmunologyShaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Yan Li
- Shaanxi Provincial Key Laboratory of Infection and Immune DiseasesShaanxi Provincial People's HospitalXi'anShaanxiChina
- Shaanxi Engineering Research Center of Cell ImmunologyShaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Zhankui Jin
- Department of OrthopedicsShaanxi Provincial People's HospitalXi'anShaanxiChina
| | - Cuixiang Xu
- Shaanxi Provincial Key Laboratory of Infection and Immune DiseasesShaanxi Provincial People's HospitalXi'anShaanxiChina
- Shaanxi Engineering Research Center of Cell ImmunologyShaanxi Provincial People's HospitalXi'anShaanxiChina
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Zhuo D, Xiao W, Tang Y, Jiang S, Geng C, Xie J, Ma X, Zhang Q, Tang K, Yu Y, Bai L, Zou H, Liu J, Wang J. Iron metabolism and arthritis: Exploring connections and therapeutic avenues. Chin Med J (Engl) 2024; 137:1651-1662. [PMID: 38867424 PMCID: PMC11268821 DOI: 10.1097/cm9.0000000000003169] [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: 12/14/2023] [Indexed: 06/14/2024] Open
Abstract
ABSTRACT Iron is indispensable for the viablility of nearly all living organisms, and it is imperative for cells, tissues, and organisms to acquire this essential metal sufficiently and maintain its metabolic stability for survival. Disruption of iron homeostasis can lead to the development of various diseases. There is a robust connection between iron metabolism and infection, immunity, inflammation, and aging, suggesting that disorders in iron metabolism may contribute to the pathogenesis of arthritis. Numerous studies have focused on the significant role of iron metabolism in the development of arthritis and its potential for targeted drug therapy. Targeting iron metabolism offers a promising approach for individualized treatment of arthritis. Therefore, this review aimed to investigate the mechanisms by which the body maintains iron metabolism and the impacts of iron and iron metabolism disorders on arthritis. Furthermore, this review aimed to identify potential therapeutic targets and active substances related to iron metabolism, which could provide promising research directions in this field.
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Affiliation(s)
- Dachun Zhuo
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
| | - Wenze Xiao
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
| | - Yulong Tang
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
| | - Shuai Jiang
- Department of Vascular Surgery, Shanghai Pudong Hospital, Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, Fudan University Pudong Medical Center, Shanghai 201399, China
| | - Chengchun Geng
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- Department of Anthropology and Human Genetics, School of Life Sciences,Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200000, China
| | - Jiangnan Xie
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- Department of Anthropology and Human Genetics, School of Life Sciences,Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200000, China
| | - Xiaobei Ma
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
| | - Qing Zhang
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
| | - Kunhai Tang
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
| | - Yuexin Yu
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
| | - Lu Bai
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
| | - Hejian Zou
- Division of Rheumatology, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
- Institute of Rheumatology, Immunology and Allergy, Allergy and Disease Research Center, Fudan University, Shanghai 200000, China
| | - Jing Liu
- Department of Rheumatology, Shanghai Pudong Hospital, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 200000, China
| | - Jiucun Wang
- Division of Rheumatology, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200000, China
- Institute of Rheumatology, Immunology and Allergy, Allergy and Disease Research Center, Fudan University, Shanghai 200000, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing 100730, China
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He B, Liao Y, Tian M, Tang C, Tang Q, Ma F, Zhou W, Leng Y, Zhong D. Identification and verification of a novel signature that combines cuproptosis-related genes with ferroptosis-related genes in osteoarthritis using bioinformatics analysis and experimental validation. Arthritis Res Ther 2024; 26:100. [PMID: 38741149 DOI: 10.1186/s13075-024-03328-3] [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: 01/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the pathogenesis of osteoarthritis (OA) is important for its prevention, diagnosis, and treatment. Therefore, we aimed to construct novel signature genes (c-FRGs) combining cuproptosis-related genes (CRGs) with ferroptosis-related genes (FRGs) to explore the pathogenesis of OA and aid in its treatment. MATERIALS AND METHODS Differentially expressed c-FRGs (c-FDEGs) were obtained using R software. Enrichment analysis was performed and a protein-protein interaction (PPI) network was constructed based on these c-FDEGs. Then, seven hub genes were screened. Three machine learning methods and verification experiments were used to identify four signature biomarkers from c-FDEGs, after which gene set enrichment analysis, gene set variation analysis, single-sample gene set enrichment analysis, immune function analysis, drug prediction, and ceRNA network analysis were performed based on these signature biomarkers. Subsequently, a disease model of OA was constructed using these biomarkers and validated on the GSE82107 dataset. Finally, we analyzed the distribution of the expression of these c-FDEGs in various cell populations. RESULTS A total of 63 FRGs were found to be closely associated with 11 CRGs, and 40 c-FDEGs were identified. Bioenrichment analysis showed that they were mainly associated with inflammation, external cellular stimulation, and autophagy. CDKN1A, FZD7, GABARAPL2, and SLC39A14 were identified as OA signature biomarkers, and their corresponding miRNAs and lncRNAs were predicted. Finally, scRNA-seq data analysis showed that the differentially expressed c-FRGs had significantly different expression distributions across the cell populations. CONCLUSION Four genes, namely CDKN1A, FZD7, GABARAPL2, and SLC39A14, are excellent biomarkers and prospective therapeutic targets for OA.
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Affiliation(s)
- Baoqiang He
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
- Southwest Medical University, Lu Zhou City, China
| | - Yehui Liao
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Minghao Tian
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Chao Tang
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Qiang Tang
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Fei Ma
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Wenyang Zhou
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China
| | - Yebo Leng
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China.
- Meishan Tianfu New Area People's Hospital, Meishan City, China.
| | - Dejun Zhong
- Department of Orthopedics, The Affiliated Hospital of Southwest Medical University, No. 25 Taping Street, Lu Zhou City, China.
- Southwest Medical University, Lu Zhou City, China.
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Ma J, Yu P, Ma S, Li J, Wang Z, Hu K, Su X, Zhang B, Cheng S, Wang S. Bioinformatics and Integrative Experimental Method to Identifying and Validating Co-Expressed Ferroptosis-Related Genes in OA Articular Cartilage and Synovium. J Inflamm Res 2024; 17:957-980. [PMID: 38370466 PMCID: PMC10871044 DOI: 10.2147/jir.s434226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/13/2024] [Indexed: 02/20/2024] Open
Abstract
Purpose Osteoarthritis (OA) is the most common joint disease worldwide and is the primary cause of disability and chronic pain in older adults.Ferroptosis is a type of programmed cell death characterized by aberrant iron metabolism and reactive oxygen species accumulation; however, its role in OA is not known. Methods To identify ferroptosis markers co-expressed in articular cartilage and synovium samples from patients with OA, in silico analysis was performed.Signature genes were analyzed and the results were evaluated using a ROC curve prediction model.The biological function, correlation between Signature genes, immune cell infiltration, and ceRNA network analyses were performed. Signature genes and ferroptosis phenotypes were verified through in vivo animal experiments and clinical samples. The expression levels of non-coding RNAs in samples from patients with OA were determined using qRT-PCR. ceRNA network analysis results were confirmed using dual-luciferase assays. Results JUN, ATF3, and CDKN1A were identified as OA- and ferroptosis-associated signature genes. GSEA analysis demonstrated an enrichment of these genes in immune and inflammatory responses, and amino acid metabolism. The CIBERSORT algorithm showed a negative correlation between T cells and these signature genes in the cartilage, and a positive correlation in the synovium. Moreover, RP5-894D12.5 and FAM95B1 regulated the expression of JUN, ATF3, and CDKN1A by competitively binding to miR-1972, miR-665, and miR-181a-2-3p. In vivo, GPX4 was downregulated in both OA cartilage and synovium; however, GPX4 and GSH were downregulated, while ferrous ions were upregulated in patient OA cartilage and synovium samples, indicating that ferroptosis was involved in the pathogenesis of OA. Furthermore, JUN, ATF3, and CDKN1A expression was downregulated in both mouse and human OA synovial and cartilage tissues. qRT-PCR demonstrated that miR-1972, RP5-894D12.5, and FAM95B1 were differentially expressed in OA tissues. Targeted interactions between miR-1972 and JUN, and a ceRNA regulatory mechanism between RP5-894D12.5, miR-1972, and JUN were confirmed by dual-luciferase assays. Conclusion This study identified JUN, ATF3, and CDKN1A as possible diagnostic biomarkers and therapeutic targets for joint synovitis and OA. Furthermore, our finding indicated that RP5-894D12.5/miR-1972/JUN was a potential ceRNA regulatory axis in OA, providing an insight into the connection between ferroptosis and OA.
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Affiliation(s)
- Jinxin Ma
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Peng Yu
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Shang Ma
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Jinjin Li
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Zhen Wang
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Kunpeng Hu
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Xinzhe Su
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Bei Zhang
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Shao Cheng
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
- Department of Arthropathy, Henan Province Hospital of Chinese Medicine (The Second Affiliated Hospital of Henan University of Chinese Medicine), Zhengzhou, People’s Republic of China
- School of Osteopathy, Henan Province Engineering Research Center of Basic and Clinical Research of Bone and Joint Repair in Chinese Medicine, Zhengzhou, People’s Republic of China
| | - Shangzeng Wang
- School of Osteopathy, Henan University of Chinese Medicine, Zhengzhou, People’s Republic of China
- Department of Arthropathy, Henan Province Hospital of Chinese Medicine (The Second Affiliated Hospital of Henan University of Chinese Medicine), Zhengzhou, People’s Republic of China
- School of Osteopathy, Henan Province Engineering Research Center of Basic and Clinical Research of Bone and Joint Repair in Chinese Medicine, Zhengzhou, People’s Republic of China
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Yan Y, He J, Cheng W. Screening of diagnostic biomarkers for ferroptosis-related osteoarthritis and construction of a risk-prognosis model. Ann Med Surg (Lond) 2024; 86:856-866. [PMID: 38333254 PMCID: PMC10849420 DOI: 10.1097/ms9.0000000000001696] [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: 09/29/2023] [Accepted: 12/24/2023] [Indexed: 02/10/2024] Open
Abstract
Background Osteoarthritis (OA) is the most prevalent and commonly chronic joint disease that frequently develops among the elderly population. It is not just a single tissue that is affected, but rather a pathology involving the entire joint. Among them, synovitis is a key pathological change in OA. Ferroptosis is a newly discovered form of cell death that results from the buildup of lipid peroxidation. However, the role and impact of it in OA are yet to be explored. Objective The key to this work is to uncover the mechanisms of ferroptosis-related OA pathogenesis and develop more novel diagnostic biomarkers to facilitate the diagnostic and therapeutic of OA. Materials and methods Download ferroptosis-related genes and OA synovial chip datasets separately from the FerrDB and Gene Expression Omnibus databases. Identify ferroptosis differentially expressed genes using R software, obtain the intersection genes through two machine learning algorithms, and obtain diagnostic biomarkers after logistic regression analysis. Verify the diagnostic and therapeutic efficacy of specific genes for OA through the construction of clinical risk prognostic models using ROC curves and nomogram. Simultaneously, correlations between specific genes and OA immune cell infiltration co-expression were constructed. Finally, verify the differential presentation of specific genes in OA and health control synovium. Results Obtain 38 ferroptosis differentially expressed genes through screening. Based on machine learning algorithms and logistic regression analysis, select AGPS, BRD4, RBMS1, and EGR1 as diagnostic biomarker genes. The diagnostic and therapeutic efficacy of the four specific genes for OA has been validated by ROC curves and nomogram of clinical risk prognostic models. The analysis of immune cell infiltration and correlation suggests a close association between specific genes and OA immune cell infiltration. Further revealing the diagnostic value of specific genes for OA by the differential presentation analysis of their differential presentation in synovial tissue from OA and health control. Conclusion This study identified four diagnostic biomarkers for OA that are associated with iron death. The establishment of a risk-prognostic model is conducive to the premature diagnosis of OA, evaluating functional recovery during rehabilitation, and guidance for subsequent treatment.
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Affiliation(s)
- Yiqun Yan
- Department of Orthopedics
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui province, People’s Republic of China
| | - Junyan He
- Department of Orthopedics
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui province, People’s Republic of China
| | - Wendan Cheng
- Department of Orthopedics
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui province, People’s Republic of China
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Huang E, Han H, Qin K, Du X. Delineation and authentication of ferroptosis genes in ventilator-induced lung injury. BMC Med Genomics 2024; 17:31. [PMID: 38254192 PMCID: PMC10804751 DOI: 10.1186/s12920-024-01804-y] [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: 08/11/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Mechanical ventilation, a critical support strategy for individuals enduring severe respiratory failure and general anesthesia, paradoxically engenders ventilator-induced lung injury (VILI). Ferrostatin-1 mitigates lung injury via ferroptosis inhibition, yet the specific ferroptosis genes contributing significantly to VILI remain obscure. METHODS Leveraging the Gene Expression Omnibus database, we acquired VILI-associated datasets and identified differentially expressed genes (DEGs). To identify the hub genes, we constructed a protein-protein interaction network and used three parameters from CytoHubba. Consequently, we identified hub genes and ferroptosis genes as ferroptosis hub genes for VILI (VFHGs). We conducted enrichment analysis and established receiver operating characteristic (ROC) curves for VFHGs. Subsequently, to confirm the correctness of the VFHGs, control group mice and VILI mouse models, as well as external dataset validation, were established. For further research, a gene-miRNA network was established. Finally, the CIBERSORT algorithm was used to fill the gap in the immune infiltration changes in the lung during VILI. RESULTS We identified 64 DEGs and 4 VFHGs (Il6,Ptgs2,Hmox1 and Atf3) closely related to ferroptosis. ROC curves demonstrated the excellent diagnostic performance of VFHGs in VILI. PCR and external dataset validation of the VILI model demonstrated the accuracy of VFHGs. Subsequently, the gene-miRNA network was successfully established. Ultimately, an Immune cell infiltration analysis associated with VILI was generated. CONCLUSIONS The results emphasize the importance of 4 VFHGs and their involvement in ferroptosis in VILI, confirming their potential as diagnostic biomarkers for VILI.
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Affiliation(s)
- Enhao Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Hanghang Han
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Ke Qin
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China
| | - Xueke Du
- Department of Anesthesiology, The Second Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, 530007, China.
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Xu L, Wang Z, Wang G. Screening of Biomarkers Associated with Osteoarthritis Aging Genes and Immune Correlation Studies. Int J Gen Med 2024; 17:205-224. [PMID: 38268862 PMCID: PMC10807283 DOI: 10.2147/ijgm.s447035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/10/2024] [Indexed: 01/26/2024] Open
Abstract
Purpose Osteoarthritis (OA) is a joint disease with a long and slow course, which is one of the major causes of disability in middle and old-aged people. This study was dedicated to excavating the cellular senescence-associated biomarkers of OA. Methods The Gene Expression Omnibus (GEO) database was searched and five datasets pertaining to OA were obtained. After removing the batch effect, the GSE55235, GSE55457, GSE82107, and GSE12021 datasets were integrated together for screening of the candidate genes by differential analysis and weighted gene co-expression network analysis (WGCNA). Next, those genes were further filtered by machine learning algorithms to obtain cellular senescence-associated biomarkers of OA. Subsequently, enrichment analyses based on those biomarkers were conducted, and we profiled the infiltration levels of 22 types immune cells with the ERSORT algorithm. A lncRNA-miRNA-mRNA regulatory and drug-gene network were constructed. Finally, we validated the senescence-associated biomarkers at both in vivo and in vitro levels. Results Five genes (BCL6, MCL1, SLC16A7, PIM1, and EPHA3) were authenticated as cellular senescence-associated biomarkers in OA. ROC curves demonstrated the reliable capacity of the five genes as a whole to discriminate OA samples from normal samples. The nomogram diagnostic model based on 5 genes proved to be a reliable predictor of OA. Single-gene GSEA results pointed to the involvement of the five biomarkers in immune-related pathways and oxidative phosphorylation in the development of OA. Immune infiltration analysis manifested that the five genes were significantly correlated with differential immune cells. Subsequently, a lncRNA-miRNA-mRNA network and gene-drug network containing were generated based on five cellular senescence-associated biomarkers in OA. Conclusion A foundation for understanding the pathophysiology of OA and new insights into OA diagnosis and treatment were provided by the identification of five genes, namely BCL6, MCL1, SLC16A7, PIM1, and EPHA3, as biomarkers associated with cellular senescence in OA.
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Affiliation(s)
- Lanwei Xu
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People’s Republic of China
- Department of Hand and Foot Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, People’s Republic of China
| | - Zheng Wang
- Department of Neurosurgery, Liaocheng Traditional Chinese Medicine Hospital, Liaocheng, 252000, People’s Republic of China
| | - Gang Wang
- Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People’s Republic of China
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Jiang D, Guo J, Liu Y, Li W, Lu D. Glycolysis: an emerging regulator of osteoarthritis. Front Immunol 2024; 14:1327852. [PMID: 38264652 PMCID: PMC10803532 DOI: 10.3389/fimmu.2023.1327852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Osteoarthritis (OA) has been a leading cause of disability in the elderly and there remains a lack of effective therapeutic approaches as the mechanisms of pathogenesis and progression have yet to be elucidated. As OA progresses, cellular metabolic profiles and energy production are altered, and emerging metabolic reprogramming highlights the importance of specific metabolic pathways in disease progression. As a crucial part of glucose metabolism, glycolysis bridges metabolic and inflammatory dysfunctions. Moreover, the glycolytic pathway is involved in different areas of metabolism and inflammation, and is associated with a variety of transcription factors. To date, it has not been fully elucidated whether the changes in the glycolytic pathway and its associated key enzymes are associated with the onset or progression of OA. This review summarizes the important role of glycolysis in mediating cellular metabolic reprogramming in OA and its role in inducing tissue inflammation and injury, with the aim of providing further insights into its pathological functions and proposing new targets for the treatment of OA.
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Affiliation(s)
- Dingming Jiang
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianan Guo
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yingquan Liu
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Wenxin Li
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
- Hangzhou Linping District Nanyuan Street Community Health Center, Hangzhou, China
| | - Dezhao Lu
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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10
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Cao J, Wang D, Yuan J, Hu F, Wu Z. Exploration of the potential mechanism of Duhuo Jisheng Decoction in osteoarthritis treatment by using network pharmacology and molecular dynamics simulation. Comput Methods Biomech Biomed Engin 2024; 27:251-265. [PMID: 37830364 DOI: 10.1080/10255842.2023.2268232] [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: 07/11/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023]
Abstract
In this study, the active ingredients of 15 Chinese herbal medicines of Duhuo Jisheng Decoction and their corresponding targets were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. The microarray data of Osteoarthritis (OA) were obtained through the GEO database for differential analysis and then a drug target-OA-related gene protein-protein interaction (PPI) network was established. The potential targets of Duhuo Jisheng Decoction in the treatment of OA were acquired by intersecting the OA-associated genes with the target genes of active ingredients. Random walk with restart (RWR) analysis of PPI networks was performed using potential targets as seed, and the top 50 genes of affinity coefficients were used as key action genes of Duhuo Jisheng Decoction in the treatment of OA. A drug-active ingredient-gene interaction network was established. AKT1, a key target of Duhuo Jisheng Decoction in the treatment of OA, was obtained by topological analysis of the gene interaction network. Molecular docking and molecular dynamics verified the binding of AKT1 to its corresponding drug active ingredients. CETSA assay demonstrated that the combination of luteolin and AKT1 increased the stability of AKT1, and the combination efficiency was high. In conclusion, the molecular mechanism of Duhuo Jisheng Decoction in treating OA featured by multiple components, targets, and pathways had been further investigated in this study, which is of significance for discovering as well as developing new drugs for this disease. The findings can also offer personalized diagnosis and treatment strategies for patients with OA in clinical practice.
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Affiliation(s)
- Jin Cao
- Department of Orthopedics, First People's Hospital of Linping District, Hangzhou, China
| | - Dayong Wang
- Department of Orthopedics, First People's Hospital of Linping District, Hangzhou, China
| | - Jianhua Yuan
- Department of Orthopedics, First People's Hospital of Linping District, Hangzhou, China
| | - Fenggen Hu
- Department of Orthopedics, First People's Hospital of Linping District, Hangzhou, China
| | - Zhen Wu
- Department of Orthopedics, Tongde Hospital of Zhejiang Province, Hangzhou, China
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11
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Zeng J, Jiang X, Jiang M, Cao Y, Jiang Y. Bioinformatics analysis of hub genes as osteoarthritis prognostic biomarkers. Sci Rep 2023; 13:22894. [PMID: 38129488 PMCID: PMC10739719 DOI: 10.1038/s41598-023-48446-1] [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: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Osteoarthritis (OA) is a progressive cartilage degradation disease, concomitant with synovitis, osteophyte formation, and subchondral bone sclerosis. Over 37% of the elderly population is affected by OA, and the number of cases is increasing as the global population ages. Therefore, the objective of this study was to identify and analyze the hub genes of OA combining with comprehensive bioinformatics analysis tools to provide theoretical basis in further OA effective therapies. Two sample sets of GSE46750 contained 12 pairs OA synovial membrane and normal samples harvested from patients as well as GSE98918 including 12 OA and non-OA patients were downloaded from the Gene Expression Omnibus database (GEO) database. Differentially expressed genes (DEGs) were identified using Gene Expression Omnibus 2R (GEO2R), followed by functional enrichment analysis, protein-protein interaction networks construction. The hub genes were identified and evaluated. An OA rat model was constructed, hematoxylin and eosin staining, safranin O/fast green staining, cytokines concentrations of serum were used to verify the model. The hub genes expression level in the knee OA samples were verified using RT-qPCR. The top 20 significantly up-regulated and down-regulated DEGs were screened out from the two datasets, respectively. The top 18 GO terms and 10 KEGG pathways were enriched. Eight hub genes were identified, namely MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA and ITGB2. Among them, the hub genes were all up-regulated in in vivo OA rat model, compared with healthy controls. The eight hub genes identified (MS4A6A, C1QB, C1QC, CD74, CSF1R, HLA-DPA1, HLA-DRA and ITGB2) were shown to be associated with OA. These genes can serve as disease markers to discriminate OA patients from healthy controls.
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Affiliation(s)
- Junfeng Zeng
- Department of Orthopedics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 17, Yongwaizheng Street, Donghu District, Nanchang City, Jiangxi Province, 330000, People's Republic of China
| | - Xinhao Jiang
- Department of Orthopedics, Yugan County Hospital, No. 1, Mianshan Avenue, Yugan County, Shangrao City, Jiangxi Province, 335100, People's Republic of China
| | - Mo Jiang
- Department of Orthopedics 10th, The Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, No. 445, Bayi Avenue, Donghu District, Nanchang City, Jiangxi Province, 330000, People's Republic of China
| | - Yuexia Cao
- Department of Orthopedics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 17, Yongwaizheng Street, Donghu District, Nanchang City, Jiangxi Province, 330000, People's Republic of China
| | - Yi Jiang
- Department of Orthopedics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, No. 17, Yongwaizheng Street, Donghu District, Nanchang City, Jiangxi Province, 330000, People's Republic of China.
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12
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Jin Z, Zhang H, Bai L, Yue L, Zhang W, Liang J, Chang B, Yang Y, Hu Z, Chen L, Guo C. Synovium is a sensitive tissue for mapping the negative effects of systemic iron overload in osteoarthritis: identification and validation of two potential targets. J Transl Med 2023; 21:661. [PMID: 37741987 PMCID: PMC10518090 DOI: 10.1186/s12967-023-04541-5] [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: 07/10/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND The prevention and treatment of osteoarthritis (OA) pose a major challenge in its research. The synovium is a critical tissue in the systematic treatment of OA. The present study aimed to investigate potential target genes and their correlation with iron overload in OA patients. METHODS The internal datasets for analysis included the microarray datasets GSE46750, GSE55457, and GSE56409, while the external datasets for validation included GSE12021 and GSE55235. The GSE176308 dataset was used to generate single-cell RNA sequencing profiles. To investigate the expression of the target genes in synovial samples, quantitative reverse transcription-PCR, western blotting, and immunohistochemical assay were conducted. ELISA was used to detect the levels of ferritin and Fe2+ in both serum and synovium. RESULTS JUN and ZFP36 were screened from the differentially expressed genes, and their mRNA were significantly reduced in the OA synovium compared to that in normal synovium. Subsequently, complex and dynamically evolving cellular components were observed in the OA synovium. The mRNA level of JUN and ZFP36 differed across various cell clusters of OA synovium and correlated with immune cell infiltration. Moreover, ferritin and Fe2+ were significantly increased in the serum and synovium of OA patients. Further, we found that JUN elevated and ZFP36 decreased at protein level. CONCLUSIONS The synovium is a sensitive tissue for mapping the adverse effects of systemic iron overload in OA. JUN and ZFP36 represent potential target genes for attenuating iron overload during OA treatment. Some discrepancies between the transcription and protein levels of JUN suggest that post-transcriptional modifications may be implicated. Future studies should also focus on the roles of JUN and ZFP36 in inducing changes in cellular components in the synovium during OA pathogenesis.
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Affiliation(s)
- Zhuangzhuang Jin
- Department of Emergence Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - He Zhang
- Department of Bone and Soft Tissue Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lunhao Bai
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lingyu Yue
- Beijing AnDing Hospital of Capital Medical University, Beijing, China
| | - Weiming Zhang
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jiajian Liang
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Bohan Chang
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Yang
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhehan Hu
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Liang Chen
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chuanji Guo
- Hospital Administration Office, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang City, Liaoning Province, China.
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13
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Wang L, Ye S, Qin J, Tang M, Dong MY, Fang J. Ferroptosis-related genes LPCAT3 and PGD are potential diagnostic biomarkers for osteoarthritis. J Orthop Surg Res 2023; 18:699. [PMID: 37723556 PMCID: PMC10507893 DOI: 10.1186/s13018-023-04128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Osteoarthritis (OA) is the most common chronic joint disease and how ferroptosis contributes to OA has garnered much attention recently. Bioinformatics promoted the discovery of ferroptosis-related biomarkers for OA. But since OA is a whole-joint disease, sensitive biomarkers for OA are still limited. We herein focused on subchondral bone, a joint component often-ignored by existing bioinformatic reports, to identify ferroptosis-related diagnostic biomarkers for OA. METHOD Microarray datasets GSE51588 and GSE55457 were downloaded from Gene Expression Omnibus database. Ferroptosis-related differential expression genes (Ferr-DEGs) between OA and normal samples were identified and their functional enrichment was analyzed. Common genes for OA diagnosis were selected from Ferr-DEGs using the combination of SVM-RFE, LASSO regression, and RandomForest machine learning algorithms. Common genes' diagnostic value was verified by receiver operating characteristic (ROC) curve and their association with immune infiltration was analyzed by CIBERSORT. Finally, candidate gene's expression was verified in chondrocytes from OA patients and in an in vitro IL-1β-induced OA model, by RT-PCR. RESULTS Two ferroptosis-related genes, LPCAT3 and PGD, were identified as OA diagnostic biomarkers and confirmed by ROC diagnostic test. The association of LPCAT3 and PGD with the infiltration of several types of immune cells was identified. The decreased expression of LPCAT3 and PGD was both confirmed in OA chondrocytes and IL-1β-induced OA condition. CONCLUSIONS We identified ferroptosis-related genes LPCAT3 and PGD as potential diagnostic biomarkers for OA, which may offer insight into the role of ferroptosis in OA and provides useful information for the diagnosis and treatment of OA.
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Affiliation(s)
- Lufei Wang
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction & Department of Orthodontics, College and Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Shouxiu Ye
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction & Department of Orthodontics, College and Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Jianliang Qin
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction & Department of Orthodontics, College and Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Min Tang
- Guangxi Key Laboratory of Oral and Maxillofacial Rehabilitation and Reconstruction & Department of Orthodontics, College and Hospital of Stomatology, Guangxi Medical University, Nanning, China
| | - Ming-You Dong
- The Key Laboratory of Molecular Pathology (For Hepatobiliary Diseases) of Guangxi, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China.
| | - Jie Fang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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14
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Yang J, Jiang T, Xu G, Wang S, Liu W. Exploring molecular mechanisms underlying the pathophysiological association between knee osteoarthritis and sarcopenia. Osteoporos Sarcopenia 2023; 9:99-111. [PMID: 37941536 PMCID: PMC10627980 DOI: 10.1016/j.afos.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 08/25/2023] [Accepted: 08/31/2023] [Indexed: 11/10/2023] Open
Abstract
Objectives Accumulating evidence indicates a strong link between knee osteoarthritis (KOA) and sarcopenia. However, the mechanisms involved have not yet been elucidated. This study primarily aims to explore the molecular mechanisms that explain the connection between these 2 disorders. Methods The gene expression profiles for KOA and sarcopenia were obtained from the Gene Expression Omnibus database, specifically from GSE55235, GSE169077, and GSE1408. Various bioinformatics techniques were employed to identify and analyze common differentially expressed genes (DEGs) across the 3 datasets. The techniques involved the analysis of Gene Ontology and pathways to enhance understanding, examining protein-protein interaction (PPI) networks, and identifying hub genes. In addition, we constructed the network of interactions between transcription factors (TFs) and genes, the co-regulatory network of TFs and miRNAs for hub genes, and predicted potential drugs. Results In total, 14 common DEGs were found between KOA and sarcopenia. Detailed information on biological processes and signaling pathways of common DEGs was obtained through enrichment analysis. After performing PPI network analysis, we discovered 4 hub genes (FOXO3, BCL6, CDKN1A, and CEBPB). Subsequently, we developed coregulatory networks for these hub genes involving TF-gene and TF-miRNA interactions. Finally, we identified 10 potential chemical compounds. Conclusions By conducting bioinformatics analysis, our study has successfully identified common gene interaction networks between KOA and sarcopenia. The potential of these findings to offer revolutionary understanding into the common development of these 2 conditions could lead to the identification of valuable targets for therapy.
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Affiliation(s)
- Jiyong Yang
- The Fifth Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tao Jiang
- Department of Orthopedics, Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, China
| | - Guangming Xu
- Department of Orthopedics, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China
| | - Shuai Wang
- The Fifth Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wengang Liu
- Department of Orthopedics, Guangdong Second Traditional Chinese Medicine Hospital, Guangzhou, China
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Sun H, Peng G, Chen K, Xiong Z, Zhuang Y, Liu M, Ning X, Yang H, Deng J. Identification of EGFR as an essential regulator in chondrocytes ferroptosis of osteoarthritis using bioinformatics, in vivo, and in vitro study. Heliyon 2023; 9:e19975. [PMID: 37810027 PMCID: PMC10559678 DOI: 10.1016/j.heliyon.2023.e19975] [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: 06/12/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Objective The mechanisms of chondrocytes ferroptosis in osteoarthritis (OA) have not yet been fully elucidated. This study aimed to identify key ferroptosis related genes (FRGs) involved in chondrocytes ferroptosis. Methods LASSO, SVM-RFE, and receiver operating characteristic curve (ROC) were performed to screen key differentially expressed FRGs (DEFRGs). Functional analyses were conducted using GO, and KEGG analyses. Unsupervised clustering analysis was used to identify ferroptosis related patterns. The CeRNA network was constructed to predict the upstream miRNAs and lncRNAs. Finally, we validated the role of EGFR in chondrocytes ferroptosis using in vivo and in vitro experiments. Results A total of 42 DEFRGs were identified between OA and normal cartilages. GO and KEGG analyses indicated that these DEFRGs were significantly engaged in ferroptosis related biological processes and pathways, such as cellular response to oxidative stress, positive regulation of programmed cell death, MAPK and PI3K-Akt signaling pathways. Moreover, four key DEFRGs, including ACSF2, AURKA, EGFR, and KLHL24, were considered as potential biomarkers of OA. Moreover, two distinct ferroptosis related patterns were determined, and a total of 882 differentially expressed genes were identified which might participate in extracellular matrix degradation and inflammatory response. In addition, the CeRNA network showed that EGFR could be competitively regulated by 3 lncRNAs and 4 miRNAs. Significantly, the expression of EGFR was downregulated in human OA cartilages, OA mouse model, and erastin induced chondrocytes. EGFR inhibition could induce the occurrence of chondrocytes ferroptosis and ECM degradation which could be reversed by the addition of Ferrostatin-1. Conclusion Our study has identified ACSF2, AURKA, EGFR, and KLHL24 as ferroptosis-related biomarkers in OA. Furthermore, we have conducted a preliminary investigation into the role of EGFR in regulating chondrocytes ferroptosis. These findings offer novel insights into the molecular mechanisms underlying OA.
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Affiliation(s)
- Hong Sun
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- Department of Emergence Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Guoxuan Peng
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Kunhao Chen
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Zhilin Xiong
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
| | - Yong Zhuang
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Miao Liu
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Xu Ning
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Hua Yang
- Department of Orthopaedics, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jin Deng
- Department of Emergence Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, China
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16
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Zhang X, Hou L, Guo Z, Wang G, Xu J, Zheng Z, Sun K, Guo F. Lipid peroxidation in osteoarthritis: focusing on 4-hydroxynonenal, malondialdehyde, and ferroptosis. Cell Death Discov 2023; 9:320. [PMID: 37644030 PMCID: PMC10465515 DOI: 10.1038/s41420-023-01613-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Osteoarthritis (OA) is a multifactorial and increasingly prevalent degenerative disease that affects the whole joint. The pathogenesis of OA is poorly understood and there is a lack of therapeutic interventions to reverse the pathological process of this disease. Accumulating studies have shown that the overproduction of reactive oxygen species (ROS) and ROS-induced lipid peroxidation are involved in the pathogenesis of OA. 4-Hydroxy-2-nonenal (4-HNE) and malondialdehyde (MDA) have received considerable attention for their role in cartilage degeneration and subchondral bone remodeling during OA development. Ferroptosis is a form of cell death characterized by a lack of control of membrane lipid peroxidation and recent studies have suggested that chondrocyte ferroptosis contributes to OA progression. In this review, we aim to discuss lipid peroxidation-derived 4-HNE and MDA in the progression of OA. In addition, the therapeutic potential for OA by controlling the accumulation of lipid peroxidation and inhibiting chondrocyte ferroptosis are discussed.
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Affiliation(s)
- Xiong Zhang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Liangcai Hou
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Zhou Guo
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Genchun Wang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Jingting Xu
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Zehang Zheng
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Kai Sun
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
| | - Fengjing Guo
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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Xie T, Ren X, Zhuang H, Jiang F, Zhang Y, Zhou P. Down-regulation of Jun induces senescence through destabilizing chromatin in osteoarthritis chondrocytes. Am J Transl Res 2023; 15:4873-4886. [PMID: 37560235 PMCID: PMC10408544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most common degenerative joint disease leading to disability worldwide. Cellular senescence is considered to be a fundamental pathogenic mechanism in the development of OA and has attracted increasing attention. However, regulatory mechanisms underlying chondrocyte senescence in OA remain unclear. METHODS Bioinformatic methods were used to screen key genes. Immunohistochemistry and the quantitative reverse transcription polymerase chain reaction were used to evaluate gene expression. RNA intervention experiments were performed to explore the functions of key genes. RESULTS We used 494 aging-associated genes provided by the Aging Atlas to identify the co-expression modules associated with age and OA. Thirty age-associated differentially expressed genes (ASDEGs) were identified. Using cytoHubba in Cytoscape, we identified Jun as the hub-ASDEG for OA chondrocytes. We confirmed the downregulation of Jun in OA rats and senescent chondrocytes by immunohistochemistry and quantitative reverse transcription polymerase chain reaction, respectively. Inhibition of proliferation and accelerated senescence were observed in chondrocytes treated with siRNA against Jun. Mechanistically, we observed micronuclei formation and reduced expression of H3K9me3 and heterochromatin protein 1gamma in siRNA-Jun-treated chondrocytes, indicating that destabilization of chromatin occurred during this treatment. CONCLUSION Jun plays a crucial role in OA development and causes senescence by destabilizing chromatin in chondrocytes. These findings provide new insights into OA progression and suggest promising therapeutic targets.
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Affiliation(s)
- Ting Xie
- Department of Women’s Health Care, Maternal and Child Health Hospital of Hubei ProvinceWuhan, Hubei, China
| | - Xunshan Ren
- Department of Orthopedics, Renmin Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Huangming Zhuang
- Department of Orthopedics, Renmin Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Fuze Jiang
- Department of Orthopedics, Renmin Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Yuelong Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Panghu Zhou
- Department of Orthopedics, Renmin Hospital of Wuhan UniversityWuhan, Hubei, China
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Zhang Y, Duan Z, Guan Y, Xu T, Fu Y, Li G. Identification of 3 key genes as novel diagnostic and therapeutic targets for OA and COVID-19. Front Immunol 2023; 14:1167639. [PMID: 37283761 PMCID: PMC10239847 DOI: 10.3389/fimmu.2023.1167639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Background Corona Virus Disease 2019 (COVID-19) and Osteoarthritis (OA) are diseases that seriously affect the physical and mental health and life quality of patients, particularly elderly patients. However, the association between COVID-19 and osteoarthritis at the genetic level has not been investigated. This study is intended to analyze the pathogenesis shared by OA and COVID-19 and to identify drugs that could be used to treat SARS-CoV-2-infected OA patients. Methods The four datasets of OA and COVID-19 (GSE114007, GSE55235, GSE147507, and GSE17111) used for the analysis in this paper were obtained from the GEO database. Common genes of OA and COVID-19 were identified through Weighted Gene Co-Expression Network Analysis (WGCNA) and differential gene expression analysis. The least absolute shrinkage and selection operator (LASSO) algorithm was used to screen key genes, which were analyzed for expression patterns by single-cell analysis. Finally, drug prediction and molecular docking were carried out using the Drug Signatures Database (DSigDB) and AutoDockTools. Results Firstly, WGCNA identified a total of 26 genes common between OA and COVID-19, and functional analysis of the common genes revealed the common pathological processes and molecular changes between OA and COVID-19 are mainly related to immune dysfunction. In addition, we screened 3 key genes, DDIT3, MAFF, and PNRC1, and uncovered that key genes are possibly involved in the pathogenesis of OA and COVID-19 through high expression in neutrophils. Finally, we established a regulatory network of common genes between OA and COVID-19, and the free energy of binding estimation was used to identify suitable medicines for the treatment of OA patients infected with SARS-CoV-2. Conclusion In the present study, we succeeded in identifying 3 key genes, DDIT3, MAFF, and PNRC1, which are possibly involved in the development of both OA and COVID-19 and have high diagnostic value for OA and COVID-19. In addition, niclosamide, ciclopirox, and ticlopidine were found to be potentially useful for the treatment of OA patients infected with SARS-CoV-2.
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Chang B, Hu Z, Chen L, Jin Z, Yang Y. Development and validation of cuproptosis-related genes in synovitis during osteoarthritis progress. Front Immunol 2023; 14:1090596. [PMID: 36817415 PMCID: PMC9932029 DOI: 10.3389/fimmu.2023.1090596] [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: 11/09/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Osteoarthritis (OA) is one of the most common refractory degenerative joint diseases worldwide. Synovitis is believed to drive joint cartilage destruction during OA pathogenesis. Cuproptosis is a novel form of copper-induced cell death. However, few studies have examined the correlations between cuproptosis-related genes (CRGs), immune infiltration, and synovitis. Therefore, we analyzed CRGs in synovitis during OA. Microarray datasets (GSE55235, GSE55457, GSE12021, GSE82107 and GSE176308) were downloaded from the Gene Expression Omnibus database. Next, we conducted differential and subtype analyses of CRGs across synovitis. Immune infiltration and correlation analyses were performed to explore the association between CRGs and immune cell abundance in synovitis. Finally, single-cell RNA-seq profiling was performed using the GSE176308 dataset to investigate the expression of CRGs in the various cell clusters. We found that the expression of five CRGs (FDX1, LIPT1, PDHA1, PDHB, and CDKN2A) was significantly increased in the OA synovium. Moreover, abundant and various types of immune cells infiltrated the synovium during OA, which was correlated with the expression of CRGs. Additionally, single-cell RNA-seq profiling revealed that the cellular composition of the synovium was complex and that their proportions varied greatly as OA progressed. The expression of CRGs differed across various cell types in the OA synovium. The current study predicted that cuproptosis may be involved in the pathogenesis of synovitis. The five screened CRGs (FDX1, LIPT1, PDHA1, PDHB, and CDKN2A) could be explored as candidate biomarkers or therapeutic targets for OA synovitis.
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Affiliation(s)
- Bohan Chang
- Department of Rheumatology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhehan Hu
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Liang Chen
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhuangzhuang Jin
- Department of Emergence Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Yang
- Department of Orthopedic Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Liu H, Deng Z, Yu B, Liu H, Yang Z, Zeng A, Fu M. Identification of SLC3A2 as a Potential Therapeutic Target of Osteoarthritis Involved in Ferroptosis by Integrating Bioinformatics, Clinical Factors and Experiments. Cells 2022; 11:3430. [PMID: 36359826 PMCID: PMC9657506 DOI: 10.3390/cells11213430] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 08/01/2023] Open
Abstract
Osteoarthritis (OA) is a type of arthritis that causes joint pain and limited mobility. In recent years, some studies have shown that the pathological process of OA chondrocytes is related to ferroptosis. Our study aims to identify and validate differentially expressed ferroptosis-related genes (DEFRGs) in OA chondrocytes and to investigate the potential molecular mechanisms. RNA-sequencing and microarray datasets were downloaded from Gene Expression Omnibus (GEO) data repository. Differentially expressed genes (DEGs) were screened by four methods: limma-voom, edgeR, DESeq2, and Wilcoxon rank-sum test. Weighted correlation network analysis (WGCNA), protein-protein interactions (PPI), and cytoHubba of Cytoscape were applied to identify hub genes. Clinical OA cartilage specimens were collected for quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, western blotting (WB), histological staining, transmission electron microscopy (TEM), and transfection. Sankey diagram was used to visualize the relationships between the expression level of SLC3A2 in the damaged area and clinical factors. Based on bioinformatics analysis, clinical factors, and experiment validation, SLC3A2 was identified as a hub gene. It was down-regulated in OA cartilage compared to normal cartilage (p < 0.05). Functional enrichment analysis revealed that SLC3A2 was associated with ferroptosis-related functions. Spearman correlation analysis showed that the expression level of SLC3A2 in the OA cartilage-damaged area was closely related to BMI, obesity grade, and Kellgren-Lawrence grade. Furthermore, in vitro experiments validated that SLC3A2 inhibited ferroptosis and suppressed cartilage degeneration in OA. In summary, we demonstrated that SLC3A2 inhibited ferroptosis and suppressed cartilage degeneration in OA. These findings provide a new idea for the study of the pathogenesis of OA, thus providing new means for the clinical diagnosis and targeted therapy of OA.
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Affiliation(s)
- Hailong Liu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zengfa Deng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Baoxi Yu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Liu
- Department of Ultrasound in Medicine, The People’s Hospital of PingYi County, Linyi 273399, China
| | - Zhijian Yang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Anyu Zeng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Ming Fu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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