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Xie X, Zhang G, Liu N. Comprehensive analysis of abnormal methylation modification differential expression mRNAs between low-grade and high-grade intervertebral disc degeneration and its correlation with immune cells. Ann Med 2024; 56:2357742. [PMID: 38819022 PMCID: PMC11146251 DOI: 10.1080/07853890.2024.2357742] [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: 01/10/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IDD) is an important cause of low back pain. The aim of this study is to identify the potential molecular mechanism of abnormal methylation-modified DNA in the progression of IDD, hoping to contribute to the diagnosis and management of IDD. METHODS Low-grade IDD (grade I-II) and high-grade IDD (grade III-V) data were downloaded from GSE70362 and GSE129789 datasets. The abnormally methylated modified differentially expressed mRNAs (DEmRNAs) were identified by differential expression analysis (screening criteria were p < .05 and |logFC| > 1) and differential methylation analysis (screening criteria were p < .05 and |δβ| > 0.1). The classification models were constructed, and the receiver operating characteristic analysis was also carried out. In addition, functional enrichment analysis and immune correlation analysis were performed and the miRNAs targeted for the abnormally methylated DEmRNAs were predicted. Finally, expression validation was performed using real-time PCR. RESULTS Compared with low-grade IDD, seven abnormal methylation-modified DEmRNAs (AOX1, IBSP, QDPR, ABLIM1, CRISPLD2, ACTC1 and EMILIN1) were identified in high-grade IDD, and the classification models of random forests (RF) and support vector machine (SVM) were constructed. Moreover, seven abnormal methylation-modified DEmRNAs and classification models have high diagnostic accuracy (area under the curve [AUC] > 0.8). We also found that AUC values of single abnormal methylation-modified DEmRNA were all lower than those of RF and SVM classification models. Pearson correlation analysis found that macrophages M2 and EMILIN1 had significant negative correlation, while macrophages M2 and IBSP had significant positive correlation. In addition, four targeted relationship pairs (hsa-miR-4728-5p-QDPR, hsa-miR-4533-ABLIM1, hsa-miR-4728-5p-ABLIM1 and hsa-miR-4534-CRISPLD2) and multiple signalling pathways (for example, PI3K-AKT signalling pathway, osteoclast differentiation and calcium signalling pathway) were also identified that may be involved in the progression of IDD. CONCLUSION The identification of abnormal methylation-modified DEmRNAs and the construction of classification models in this study were helpful for the diagnosis and management of IDD progression.
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Affiliation(s)
- Xuehu Xie
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Guoqiang Zhang
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
| | - Ning Liu
- Department of Orthopedics, Beijing Friendship Hospital, Capital Medical University, Xicheng District, Beijing, China
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Bing T, Shanlin X, Jisheng W, Jie H, Ruichao C, Zhiwei Z, Bin Y, Zhaoxin M, Zhenming H, Nian Z. Dysregulated lipid metabolism and intervertebral disc degeneration: the important role of ox-LDL/LOX-1 in endplate chondrocyte senescence and calcification. Mol Med 2024; 30:117. [PMID: 39123116 PMCID: PMC11311918 DOI: 10.1186/s10020-024-00887-8] [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: 04/28/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Lipid metabolism disorders are associated with degeneration of multiple tissues and organs, but the mechanism of crosstalk between lipid metabolism disorder and intervertebral disc degeneration (IDD) has not been fully elucidated. In this study we aim to investigate the regulatory mechanism of abnormal signal of lipid metabolism disorder on intervertebral disc endplate chondrocyte (EPC) senescence and calcification. METHODS Human intervertebral disc cartilage endplate tissue, cell model and rat hyperlipemia model were performed in this study. Histology and immunohistochemistry were used to human EPC tissue detection. TMT-labelled quantitative proteomics was used to detect differential proteins, and MRI, micro-CT, safranin green staining and immunofluorescence were performed to observe the morphology and degeneration of rat tail intervertebral discs. Flow cytometry, senescence-associated β-galactosidase staining, alizarin red staining, alkaline phosphatase staining, DCFH-DA fluorescent probe, and western blot were performed to detect the expression of EPC cell senescence, senescence-associated secretory phenotype, calcification-related proteins and the activation of cell senescence-related signaling pathways. RESULTS Our study found that the highly expressed oxidized low-density lipoprotein (ox-LDL) and Lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1) in human degenerative EPC was associated with hyperlipidemia (HLP). TMT-labelled quantitative proteomics revealed enriched pathways such as cell cycle regulation, endochondral bone morphogenesis and inflammation. The rat model revealed that HLP could induce ox-LDL, LOX-1, senescence and calcification markers high expression in EPC. Moreover, we demonstrated that ox-LDL-induced EPCs senescence and calcification were dependent on the LOX-1 receptor, and the ROS/P38-MAPK/NF-κB signaling pathway was implicated in the regulation of senescence induced by ox-LDL/LOX-1 in cell model. CONCLUSIONS So our study revealed that ox-LDL/LOX-1-induced EPCs senescence and calcification through ROS/P38-MAPK/NF-κB signaling pathway, providing information on understanding the link between lipid metabolism disorders and IDD.
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Affiliation(s)
- Tan Bing
- Department of Spine Surgery, The Third Hospital of Mian Yang, Sichuan Mental Health Center, 621000, Mianyang, People's Republic of China
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Xiang Shanlin
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Wang Jisheng
- Department of Pharmacy, The Third Hospital of Mian Yang, Sichuan Mental Health Center, 621000, Mianyang, People's Republic of China
| | - Hao Jie
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Cao Ruichao
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Zhang Zhiwei
- Department of Radiology, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Yu Bin
- Department of Radiology, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Ma Zhaoxin
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Hu Zhenming
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China
| | - Zhou Nian
- Department of Orthopedics, Orthopedic Laboratory of Chongqing Medical University, The First Affiliated Hospital of Chongqing Medical University, 400000, Chongqing, People's Republic of China.
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Luo J, Jin G, Cui S, Wang H, Liu Q. Regulatory mechanism of FCGR2A in macrophage polarization and its effects on intervertebral disc degeneration. J Physiol 2024; 602:1341-1369. [PMID: 38544414 DOI: 10.1113/jp285871] [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: 10/28/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024] Open
Abstract
Intervertebral disc degeneration (IDD) poses a significant health burden, necessitating a deeper understanding of its molecular underpinnings. Transcriptomic analysis reveals 485 differentially expressed genes (DEGs) associated with IDD, underscoring the importance of immune regulation. Weighted gene co-expression network analysis (WGCNA) identifies a yellow module strongly correlated with IDD, intersecting with 197 DEGs. Protein-protein interaction (PPI) analysis identifies ITGAX, MMP9 and FCGR2A as hub genes, predominantly expressed in macrophages. Functional validation through in vitro and in vivo experiments demonstrates the pivotal role of FCGR2A in macrophage polarization and IDD progression. Mechanistically, FCGR2A knockdown suppresses M1 macrophage polarization and NF-κB phosphorylation while enhancing M2 polarization and STAT3 activation, leading to ameliorated IDD in animal models. This study sheds light on the regulatory function of FCGR2A in macrophage polarization, offering novel insights for IDD intervention strategies. KEY POINTS: This study unveils the role of FCGR2A in intervertebral disc (IVD) degeneration (IDD). FCGR2A knockdown mitigates IDD in cellular and animal models. Single-cell RNA-sequencing uncovers diverse macrophage subpopulations in degenerated IVDs. This study reveals the molecular mechanism of FCGR2A in regulating macrophage polarization. This study confirms the role of the NF-κB/STAT3 pathway in regulating macrophage polarization in IDD.
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Affiliation(s)
- Jiaying Luo
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Guoxin Jin
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Shaoqian Cui
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Huan Wang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
| | - Qi Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, P. R. China
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Hu K, Shu Y, Feng Z, Zou M, Luo J, Wei Z, Peng J, Hao L. Role of lipid metabolism gene KLF4 in osteoarthritis. Clin Rheumatol 2024; 43:453-464. [PMID: 37608136 DOI: 10.1007/s10067-023-06742-1] [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: 01/31/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
INTRODUCTION Osteoarthritis (OA) is a common degenerative disease of joints, which can appear in almost any joint of the body. Therefore, the widespread occurrence of this disease has a huge impact on the lives of patients around the world. As an important part of metabolism, lipid metabolism is closely related to the occurrence and development of osteoarthritis. METHOD We screened UGCG and KLF4 based on weighted co-expression network analysis (WGCNA) and SVM-REF analysis. The data from Gene Expression Omnibus (GEO) and single-cell data verified the expression of these two genes. We analyzed KLF4-related genes and established a diagnosis model of OA related to lipid metabolism through the least absolute shrinkage and selection operator (LASSO) analysis. RT-PCR was used to verify the expression of KLF4 in osteoarthritis. RESULTS Ten important lipid metabolism related genes (LMRGs) in OA were obtained. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that they are involve in the formation of immune microenvironment in osteoarthritis. CIBERSORT analysis revealed that there were significant differences in the immune microenvironment between osteoarthritis patients and normal controls. RT-PCR results showed that the expression of KLF4 in OA samples was lower than that in normal samples. The diagnostic model can be used to diagnose OA patients well. CONCLUSIONS Overall, we demonstrated the potential relationship between the abnormal lipid metabolism and the pathological process of OA. Finally, we identified KLF4 as our significant LMRG and constructed a KLF4-related scoring model to accurately diagnose OA. In conclusion, therapy strategies targeting on regulating lipid metabolism may become a key factor in treating OA. Key Points (a) We identified the significant LMRG KLF4 and constructed a novel KLF4-related scoring model for the accuracy diagnosis of OA. (b) The potential relationship between lipid metabolism and the immune microenvironment in OA was demonstrated in our research. (c) The relationship of lipid metabolism and OA has been further improved in our research and provided novel insight for the diagnosis and therapy for OA patients.
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Affiliation(s)
- Kaibo Hu
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Yuan Shu
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Zuxi Feng
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Mi Zou
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Jiazhe Luo
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Ziyue Wei
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China
| | - Jie Peng
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China.
- The Second Clinical Medical College of Nanchang University, Nanchang, 330006, Jiangxi Province, China.
- Department of Sports Medicine, Huashan Hospital, Fudan University, 200040, Shanghai, China.
| | - Liang Hao
- Departments of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi Province, China.
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Wang N, Mi Z, Chen S, Fang X, Xi Z, Xu W, Xie L. Analysis of global research hotspots and trends in immune cells in intervertebral disc degeneration: A bibliometric study. Hum Vaccin Immunother 2023; 19:2274220. [PMID: 37941392 PMCID: PMC10760394 DOI: 10.1080/21645515.2023.2274220] [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: 07/06/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Intervertebral disc degeneration is an important pathological basis for spinal degenerative diseases. The imbalance of the immune microenvironment and the involvement of immune cells has been shown to lead to nucleus pulposus cells death. This article presents a bibliometric analysis of studies on immune cells in IDD in order to clarify the current status and hotspots. We searched the WOSCC, Scopus and PubMed databases from 01/01/2001 to 08/03/2023. We analyzed and visualized the content using software such as Citespace, Vosviewer and the bibliometrix. This study found that the number of annual publications is increasing year on year. The journal study found that Spine had the highest number of articles and citations. The country/regions analysis showed that China had the highest number of publications, the USA had the highest number of citations and total link strength. The institutional analysis found that Shanghai Jiao Tong University and Huazhong University of Science Technology had the highest number of publications, Tokai University had the highest citations, and the University of Bern had the highest total link strength. Sakai D and Risbud MV had the highest number of publications. Sakai D had the highest total link strength, and Risbud MV had the highest number of citations. The results of the keyword analysis suggested that the current research hotspots and future directions continue to be the study of the mechanisms of immune cells in IDD, the therapeutic role of immune cells in IDD and the role of immune cells in tissue engineering for IDD.
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Affiliation(s)
- Nan Wang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Zehua Mi
- Hospital for Skin Diseases, Institute of Dermatology Chinese Academy of Medical Sciences, Peking Union Medical College, Nanjing, China
| | - Shuang Chen
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Xiaoyang Fang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Zhipeng Xi
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Wenqiang Xu
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
| | - Lin Xie
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, P.R. China
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Zhao Y, Mu Y, Zou Y, Lei X, Ji R, Wei B, Wei T, Lu T, He Z, Wang X, Li W, Gao B. Integrated analysis of single-cell transcriptome and structural biology approach reveals the dynamics changes of NP subtypes and roles of Menaquinone in attenuating intervertebral disc degeneration. J Biomol Struct Dyn 2023:1-24. [PMID: 37902557 DOI: 10.1080/07391102.2023.2275172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/18/2023] [Indexed: 10/31/2023]
Abstract
Intervertebral disc degeneration (IDD) is a progressive and chronic disease, the mechanisms have been studied extensively as a whole, while the cellular heterogeneity of cells in nucleus pulposus (NP) tissues remained controversial for a long time. This study conducted integrated analysis through single-cell sequencing analysis, weighted gene co-expression network analysis (WGCNA), and differential expression analysis, to systematically decipher the longitudinal alterations of distinct NP subtypes, and also analyzed the most essential genes in the development of IDD. Then, this study further conducted structural biology method to discover the potential lead compounds through a suite of advanced approaches like high-throughput screening (HTVS), pharmaceutical characteristics assessment, CDOCKER module as well as molecular dynamics simulation, etc., aiming to ameliorate the progression of IDD. Totally 5 NP subpopulations were identified with distinct biological functions based on their unique gene expression patterns. The predominant dynamics changes mainly involved RegNPs and EffNPs, the RegNPs were mainly aggregated in normal NP tissues and drastically decreased in degenerative NP, while EffNPs, as pathogenic subtype, exhibited opposite phenomenon. Importantly, this study further reported the essential roles of Menaquinone in alleviating degenerative NP cells for the first time, which could provide solid evidence for the application of nutritional therapy in the treatment of IDD. This study combined scRNA-seq, bulk-RNA seq and HTVS techniques to systematically decipher the longitudinal changes of NP subtypes during IDD. EffNPs were considered to be 'chief culprit' in IDD progression, while the novel natural drug Menaquinone could reverse this phenomenon.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yingjing Zhao
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Yuxue Mu
- Aerospace Clinical Medical Center, School of Aerospace Medicine, Air Force Medical University, Xi'an, China
| | - Yujia Zou
- China-Japan Union Hospital, Jilin University, Jilin, China
- Department of Cardiology, Xinhua Hospital Affiliated to School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Xin Lei
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Rui Ji
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Bingqian Wei
- Basic Medical College, Air Force Medical University, Xi'an, China
| | - Tianyu Wei
- Basic Medical College, Air Force Medical University, Xi'an, China
| | - Tianxing Lu
- Zonglian College, Xi'an Jiaotong University, Xi'an, China
| | - Zhijian He
- Department of Sports Teaching and Research, Lanzhou University, Lanzhou, China
| | - Xinhui Wang
- Department of Oncology, The Fifth Affiliated Hospital of Xinxiang Medical College, Xinxiang, China
| | - Weihang Li
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Bo Gao
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
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Yin Y, He M, Huang Y, Xie X. Transcriptomic analysis identifies CYP27A1 as a diagnostic marker for the prognosis and immunity in lung adenocarcinoma. BMC Immunol 2023; 24:37. [PMID: 37817081 PMCID: PMC10565965 DOI: 10.1186/s12865-023-00572-1] [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: 07/10/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The association between lipid metabolism disorder and carcinogenesis is well-established, but there is limited research on the connection between lipid metabolism-related genes (LRGs) and lung adenocarcinoma (LUAD). The objective of our research was to identify LRGs as the potential biomarkers for prognosis and assess their impact on immune cell infiltration in LUAD. METHODS We identified novel prognostic LRGs for LUAD patients via the bioinformatics analysis. CYP27A1 expression level was systematically evaluated via various databases, such as TCGA, UALCAN, and TIMER. Subsequently, LinkedOmics was utilized to perform the CYP27A1 co-expression network and GSEA. ssGSEA was conducted to assess the association between infiltration of immune cells and CYP27A1 expression. CYP27A1's expression level was validated by qRT-PCR analysis. RESULTS CYP27A1 expression was decreased in LUAD. Reduced CYP27A1 expression was linked to unfavorable prognosis in LUAD. Univariate and multivariate analyses indicated that CYP27A1 was an independent prognostic biomarker for LUAD patients. GSEA results revealed a positive correlation between CYP27A1 expression and immune-related pathways. Furthermore, CYP27A1 expression was positively correlated with the infiltration levels of most immune cells. CONCLUSION CYP27A1 is a potential biomarker for LUAD patients, and our findings provided a novel perspective to develop the prognostic marker for LUAD patients.
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Affiliation(s)
- Yi Yin
- Department of Medical Oncology, Clinical Oncology School of, Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Muqun He
- Department of Medical Oncology, Clinical Oncology School of, Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Yunjian Huang
- Department of Medical Oncology, Clinical Oncology School of, Fujian Medical University, Fujian Cancer Hospital, Fuzhou, 350014, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.
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Liu XW, Xu HW, Yi YY, Zhang SB, Wang SJ. Role of ferroptosis and immune infiltration in intervertebral disc degeneration: novel insights from bioinformatics analyses. Front Cell Dev Biol 2023; 11:1170758. [PMID: 37736497 PMCID: PMC10509768 DOI: 10.3389/fcell.2023.1170758] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Background: Intervertebral disc degeneration (IVDD), which contributes to stenosis of the spinal segment, commonly causes lower back pain. The process of IVDD degradation entails gradual structural adjustments accompanied by extreme transformations in metabolic homeostasis. However, the molecular and cellular mechanisms associated with IVDD are poorly understood. Methods: The RNA-sequencing datasets GSE34095 and GSE56081 were obtained from the Gene Expression Omnibus (GEO) database. Ferroptosis-related differentially expressed genes (DEGs) were identified from these gene sets. The protein-protein interaction (PPI) network was established and visualized using the STRING database and Cytoscape software, and the key functional modules of ferroptosis-related genes were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the DEGs. Weighted gene co-expression network analysis (WGCNA), immune infiltration analysis in the GEO database, and other GSE series were used as validation datasets. The xCELL algorithm was performed to investigate the immune cell infiltration differences between the degenerated IVDD and control groups. Results: The major genes involved in nucleus pulposus tissue immune infiltration and ferroptosis-related genes were mined by bioinformatics analysis. A total of 3,056 DEGs were obtained between the IVDD tissue and control groups. The DEGs were enriched in the cell cycle; apoptosis; necroptosis; and the PI3K-Akt, Hippo, and HIF-1 signaling pathways. PCR and Western blot techniques were utilized to confirm the differential ferroptosis-related genes. The results indicated that the protein expression levels of NCOA4 and PCBP1 were elevated, while the protein expression level of GPX4 was reduced in NPCs following IL-1β treatment. Our study has found that severe disc tissue degeneration leads to a noteworthy increase in the expression of CD8A in naive T cells, CCR7 in memory CD4+ cells, GZMB in natural killer (NK) cells, and CD163 and CD45 in macrophages. Conclusion: Our data demonstrate that ferroptosis occurs in IVDD, suggesting that ferroptosis may also increase IVDD improvement by triggering immune infiltration. This work was conducted to further understand IVDD pathogenesis and identify new treatment strategies.
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Affiliation(s)
- Xiao-Wei Liu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hao-Wei Xu
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yu-Yang Yi
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shu-Bao Zhang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shan-Jin Wang
- Department of Spinal Surgery, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Orthopedic, East Hospital, Ji’an Hospital, Jinggangshan University School of Medicine, Jiangxi, China
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Tao Q, Zhu Y, Wang T, Deng Y, Liu H, Wu J. Identification and analysis of lipid metabolism-related genes in allergic rhinitis. Lipids Health Dis 2023; 22:105. [PMID: 37480069 PMCID: PMC10362667 DOI: 10.1186/s12944-023-01825-z] [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: 01/10/2023] [Accepted: 04/28/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Studies have shown that the lipid metabolism mediator leukotriene and prostaglandins are associated with the pathogenesis of allergic rhinitis (AR). The aim of this study was to identify key lipid metabolism-related genes (LMRGs) related to the diagnosis and treatment of AR. MATERIALS AND METHODS AR-related expression datasets (GSE75011, GSE46171) were downloaded through the Gene Expression Omnibus (GEO) database. First, weighted gene co-expression network analysis (WGCNA) was used to get AR-related genes (ARRGs). Next, between control and AR groups in GSE75011, differentially expressed genes (DEGs) were screened, and DEGs were intersected with LMRGs to obtain lipid metabolism-related differentially expressed genes (LMR DEGs). Protein-protein interaction (PPI) networks were constructed for these LMR DEGs. Hub genes were then identified through stress, radiality, closeness and edge percolated component (EPC) analysis and intersected with the ARRGs to obtain candidate genes. Biomarkers with diagnostic value were screened via receiver operating characteristic (ROC) curves. Differential immune cells screened between control and AR groups were then assessed for correlation with the diagnostic genes, and clinical correlation analysis and enrichment analysis were performed. Finally, real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was made on blood samples from control and AR patients to validate these identified diagnostic genes. RESULTS 73 LMR DEGs were obtained, which were involved in biological processes such as metabolism of lipids and lipid biosynthetic processes. 66 ARRGs and 22 hub genes were intersected to obtain four candidate genes. Three diagnostic genes (LPCAT1, SGPP1, SMARCD3) with diagnostic value were screened according to the AUC > 0.7, with markedly variant between control and AR groups. In addition, two immune cells, regulatory T cells (Treg) and T follicular helper cells (TFH), were marked variations between control and AR groups, and SMARCD3 was significantly associated with TFH. Moreover, SMARCD3 was relevant to immune-related pathways, and correlated significantly with clinical characteristics (age and sex). Finally, RT-qPCR results indicated that changes in the expression of LPCAT1 and SMARCD3 between control and AR groups were consistent with the GSE75011 and GSE46171. CONCLUSION LPCAT1, SGPP1 and SMARCD3 might be used as biomarkers for AR.
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Affiliation(s)
- Qilei Tao
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China
| | - Yajing Zhu
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China
| | - Tianyu Wang
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China
| | - Yue Deng
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China
| | - Huanhai Liu
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China.
| | - Jian Wu
- Department of Otolaryngology, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, 200003, China.
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Tang T, He Z, Zhu Z, Wang F, Chen H, Zhang F, Zhou J, Wang J, Li B, Liu X, Zhou Z, Liu S. Identification of novel gene signatures and immune cell infiltration in intervertebral disc degeneration using bioinformatics analysis. Front Mol Biosci 2023; 10:1169718. [PMID: 37520321 PMCID: PMC10380950 DOI: 10.3389/fmolb.2023.1169718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023] Open
Abstract
Background: Intervertebral disc degeneration (IDD) is the leading cause of lower back pain, and an overall understanding of the molecular mechanisms related to IDD is still lacking. The purpose of this study was to explore gene signatures and immune cell infiltration related to IDD via bioinformatics analysis. Methods: A total of five expression profiles of mRNA and non-coding RNA were downloaded from the Gene Expression Omnibus (GEO) database. The potentially involved lncRNA/circRNA-miRNA-mRNA networks and protein-protein interaction networks were constructed by miRNet, circBank, STRING, and the Cytoscape database. Gene ontology, Kyoto Encyclopaedia of Genes and Genomes Analysis, Gene Set Enrichment Analysis, Gene Set Variation Analysis, Immune Infiltration Analysis, and Drug-Gene Interaction were used to analyse the top 20 hub genes. RT-qPCR was conducted to confirm the 12 differential expressions of genes both in the nucleus pulposus and annulus fibrosus tissues Results: There were 346 differentially expressed mRNAs, 12 differentially expressed miRNAs, 883 differentially expressed lncRNAs, and 916 differentially expressed circRNAs in the GEO database. Functional and enrichment analyses revealed hub genes associated with platelet activation, immune responses, focal adhesion, and PI3K-Akt signalling. The apoptotic pathway, the reactive oxygen species pathway, and oxidative phosphorylation play an essential role in IDD. Immune infiltration analysis demonstrated that the Treg cells had significant infiltration, and three levels of immune cells, including dendritic cells, Th2 cells, and tumour-infiltrating lymphocytes, were inhibited in IDD. Drug-gene interaction analysis showed that COL1A1 and COL1A2 were targeted by collagenase clostridium histolyticum, ocriplasmin, and PDGFRA was targeted by 66 drugs or molecular compounds. Finally, 24 cases of IDD tissues and 12 cases of normal disc tissues were collected, and the results of RT-qPCR were consistent with the bioinformatics results. Conclusion: Our data indicated that the 20 hub genes and immune cell infiltration were involved in the pathological process of IDD. In addition, the PDGFRA and two potential drugs were found to be significant in IDD development.
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Affiliation(s)
- Tao Tang
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhongyuan He
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhengya Zhu
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fuan Wang
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongkun Chen
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fu Zhang
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jiaxiang Zhou
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jianmin Wang
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Baoliang Li
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xizhe Liu
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiyu Zhou
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shaoyu Liu
- Innovation Platform of Regeneration and Repair of Spinal Cord and Nerve Injury, Department of Orthopaedic Surgery, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Xu WB, Kotheeranurak V, Chen DQ, Sun NK, Cai DX, Chen CM, Lin GX, Rui G. Pan-cancer analysis of the intervertebral-disc-degeneration-related innate immunity gene NAIP. PLoS One 2023; 18:e0286647. [PMID: 37267294 DOI: 10.1371/journal.pone.0286647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/15/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IDD) is a progressive chronic condition that commonly causes low back pain. Cancer is among the primary reasons for deaths worldwide. Our purpose was to identify the characteristic genes of IDD and explore the potential association between IDD and cancer. METHODS Immune cell infiltration and differentially expressed analysis were conducted utilizing data from the GSE124272 database. Enrichment analysis of differentially expressed genes (DEGs) was performed to explore the possible mechanisms underlying IDD development. Moreover, weighted gene correlation network analysis (WGCNA) was applied to select IDD-related hub genes. The immune-related key genes were determined by intersecting DEGs, IDD-related hub genes, and immune genes. Subsequently, machine learning models based on these genes were built to identify and verify the characteristic genes. RNA sequencing and clinical data of 33 carcinoma categories were obtained from the Cancer Genome Atlas (TCGA). The association between NAIP expression and prognosis was calculated using the Kaplan-Meier analysis. To gain a deeper understanding of the impact of NAIP in tumor immunotherapy, the association between NAIP and immune infiltration and two immunotherapeutic biomarkers were explored. Ultimately, the association between NAIP and immunotherapeutic response was investigated utilizing two independent cohorts. RESULTS NAIP was identified as an immune-related characteristic gene between IDD and normal intervertebral disc tissue. In certain carcinoma categories, NAIP expression levels were elevated (4/33) and significantly correlated to the respective tumor stage (4/21). Survival analysis revealed that the expression levels of NAIP have prognostic significance in different cancer types. Generally, NAIP presented a strong association with immune cell infiltration and modulators. NAIP may influence immunotherapy effects through tumor mutational burden and microsatellite instability. No remarkable association between NAIP and immunotherapy response was found in either cohort. CONCLUSION Our study is the first to identify NAIP as an immune-related characteristic gene. Pan-cancer analysis revealed that NAIP could serve as a novel clinical prognostic marker and therapeutic target for a variety of carcinoma categories, reducing the risk of IDD in tumor patients.
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Affiliation(s)
- Wen-Bin Xu
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Vit Kotheeranurak
- Department of Orthopedics, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
- Center of Excellence in Biomechanics and Innovative Spine Surgery, Chulalongkorn University, Bangkok, Thailand
| | - Ding-Qiang Chen
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Nai-Kun Sun
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Di-Xin Cai
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Chien-Min Chen
- Division of Neurosurgery, Department of Surgery, Changhua Christian Hospital, Changhua, Taiwan
- Department of Leisure Industry Management, National Chin-Yi University of Technology, Taichung, Taiwan
- School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Guang-Xun Lin
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
| | - Gang Rui
- Department of Orthopedics, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, Fujian, China
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Li W, Zhao Y, Wang Y, He Z, Zhang L, Yuan B, Li C, Luo Z, Gao B, Yan M. Deciphering the sequential changes of monocytes/macrophages in the progression of IDD with longitudinal approach using single-cell transcriptome. Front Immunol 2023; 14:1090637. [PMID: 36817437 PMCID: PMC9929188 DOI: 10.3389/fimmu.2023.1090637] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Intervertebral disk degeneration (IDD) is a chronic inflammatory disease with intricate connections between immune infiltration and oxidative stress (OS). Complex cell niches exist in degenerative intervertebral disk (IVD) and interact with each other and regulate the disk homeostasis together. However, few studies have used longitudinal approach to describe the immune response of IDD progression. Here, we conducted conjoint analysis of bulk-RNA sequencing and single-cell sequencing, together with a series of techniques like weighted gene co-expression network analysis (WGCNA), immune infiltration analysis, and differential analysis, to systematically decipher the difference in OS-related functions of different cell populations within degenerative IVD tissues, and further depicted the longitudinal alterations of immune cells, especially monocytes/macrophages in the progression of IDD. The OS-related genes CYP1A1, MMP1, CCND1, and NQO1 are highly expressed and might be diagnostic biomarkers for the progression of IDD. Further landscape of IVD microenvironment showed distinct changes in cell proportions and characteristics at late degeneration compared to early degeneration of IDD. Monocytes/macrophages were classified into five distinct subpopulations with different roles. The trajectory lineage analysis revealed transcriptome alterations from effector monocytes/macrophages and regulatory macrophages to other subtypes during the evolution process and identified monocytes/macrophage subpopulations that had rapidly experienced the activation of inflammatory or anti-inflammatory responses. This study further proposed that personalized therapeutic strategies are needed to be formulated based on specific monocyte/macrophage subtypes and degenerative stages of IDD.
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Affiliation(s)
- Weihang Li
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Yingjing Zhao
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yongchun Wang
- Department of Aerospace Medical Training, School of Aerospace Medicine, Air Force Medical University, Xi'an, China
| | - Zhijian He
- Department of Sports Teaching and Research, Lanzhou University, Lanzhou, China
| | - Linyuan Zhang
- Department of Nursing, Air Force Medical University, Xi'an, China
| | - Bin Yuan
- Department of Spine Surgery, Daxing Hospital, Xi'an, Shaanxi, China
| | - Chengfei Li
- Department of Aerospace Medical Training, School of Aerospace Medicine, Air Force Medical University, Xi'an, China
| | - Zhuojing Luo
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Bo Gao
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Ming Yan
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi'an, China
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Zhang F, Cui D, Wang K, Cheng H, Zhai Y, Jiao W, Wang Z, Cui X, Yu H. Identifification and validation of ferroptosis signatures and immune infifiltration characteristics associated with intervertebral disc degeneration. Front Genet 2023; 14:1133615. [PMID: 36911415 PMCID: PMC9992550 DOI: 10.3389/fgene.2023.1133615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
Ferroptosis and immune infiltration play an important role in the pathogenesis of intervertebral disc degeneration (IDD). However, there is still a lack of comprehensive analysis on the interaction between ferroptosis-related genes (FRGs) and immune microenvironment in IDD patients. Therefore, this study aims to explore the correlation between FRGs characteristics and immune infiltration in the progression of IDD. The expression profiles (GSE56081 and GSE70362) and FRGs were downloaded from the comprehensive gene expression omnibus (GEO) and FerrDb database, respectively, and the differences were analyzed using R. The intersection of IDD related differential genes (DEGs) and FRGs was taken as differentially expressed FRGs (DE-FRGs) and GO and KEGG enrichment analysis was conducted. Then, we used least absolute shrinkage and selection operator (LASSO) regression algorithm and support vector machine (SVM) algorithm to screen feature genes and draw ROC curve judge the diagnostic value of key DE-FRGs. Then CIBERSORT algorithm is used to evaluate the infiltration of immune cells and analyze the correlation between key DE-FRGs and immune infiltration. Based on the analysis results, we conducted single gene GSEA analysis on key DE-FRGs. RT-PCR and immunohistochemistry further verified the clinical value of the results of biochemical analysis and screening. Seven key DE-FRGs were screened, including the upregulated genes NOX4 and PIR, and the downregulated genes TIMM9, ATF3, ENPP2, FADS2 and TFAP2A. Single gene GSEA analysis further elucidates the role of DE-FRGs in IDD associated with ferroptosis. Correlation analysis showed that seven key DE-FRGs were closely related to immune infiltration in the development of IDD. Finally, RT-PCR and immunohistochemical staining showed that NOX4, ENPP2, FADS2 and TFAP2A were statistically significant differences. In this study, we explored the connection between ferroptosis related characteristics and immune infiltration in IDD, and confirmed that NOX4, ENPP2, FADS2, and TFAP2A may become biomarkers and potential therapeutic targets for IDD.
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Affiliation(s)
- Feng Zhang
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
| | - Di Cui
- Medical School of Fuyang Normal University, Fuyang, Anhui, China
| | - Kangkang Wang
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
| | - Huimin Cheng
- Medical School of Fuyang Normal University, Fuyang, Anhui, China
| | - Yunlei Zhai
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
| | - Wei Jiao
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
| | - Zhaodong Wang
- Anhui Province Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, Anhui, China.,Department of Orthopedics, the First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Xilong Cui
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
| | - Haiyang Yu
- Department of Orthopedics, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.,Clinical Research Center for Spinal Deformity of Anhui Province, Fuyang, Anhui, China
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Metabolism-Related Gene TXNRD1 Regulates Inflammation and Oxidative Stress Induced by Cigarette Smoke through the Nrf2/HO-1 Pathway in the Small Airway Epithelium. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7067623. [PMID: 36578523 PMCID: PMC9792251 DOI: 10.1155/2022/7067623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
Chronic obstructive pulmonary disease (COPD), a small airway disease, is regarded as a metabolic disorder. To further uncover the metabolic profile of COPD patients, it is necessary to identify metabolism-related differential genes in small airway epithelium (SAE) of COPD. Metabolism-related differential genes in SAE between COPD patients and nonsmokers were screened from GSE128708 and GSE20257 datasets. KEGG, GO, and PPI analyses were performed to evaluate the pathway enrichment, term enrichment, and protein interaction of candidate metabolism-related differential genes, respectively. RT-PCR was used to verify the mRNA expression of the top ten differential genes. Western blotting was used to evaluate the protein expression of TXNRD1. TXNRD1 inhibitor auranofin (AUR) was used to assess the impact of TXNRD1 on oxidative stress and inflammation induced by cigarette smoke extraction (CSE). Twenty-four metabolism-related differential genes were selected. ALDH3A1, AKR1C3, CYP1A1, AKC1C1, CPY1B1, and TXNRD1 in the top ten genes were significantly upregulated after CSE simulation for 24 h in human bronchial epithelial (16HBE) cells. Among them, CYP1A1 and TXNRD1 also have a significant upregulation in primary SAE after simulation of CSE for 24 h. The overexpression of protein TXNRD1 has also been detected in 16HBE cells, primary SAE stimulated with CSE, and mouse lung exposed to cigarette smoke (CS). Additionally, inhibition of TXNRD1 with 0.1 μM AUR alleviated the expression of IL-6 and reactive oxygen species (ROS) induced by CSE by activating the Nrf2/HO-1 pathway in 16HBE cells. This study identified twenty-four metabolism-related differential genes associated with COPD. TXNRD1 might participate in the oxidative stress and inflammation induced by CS by regulating the activation of the Nrf2/HO-1 pathway.
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Fang X, Tang T, Sun D, Chen S, Wang N, Xie L. Comprehensive analysis of potential ceRNA network and immune cell infiltration in intervertebral disc degeneration. J Orthop Surg Res 2022; 17:432. [PMID: 36175893 PMCID: PMC9524080 DOI: 10.1186/s13018-022-03331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Background Intervertebral disc degeneration (IDD) has become a serious public health problem, the mechanism of which is complex and still unclear. We aimed to construct a ceRNA network related to IDD to explore its pathogenesis. Methods We downloaded the GSE67566, GSE63492, GSE116726 and GSE124272 datasets from GEO database, and obtained the differentially expressed RNAs. Then, we constructed a ceRNA network and the KEGG and GO enrichment analysis were performed. Finally, we performed immune cell infiltration analysis on the GSE124272 dataset and analysed the correlation between immune cell abundance and hub genes expression levels. Results The ceRNA network included three down-regulated circRNAs: hsa_circ_0074817, hsa_circ_0002702, hsa_circ_0003600, three up-regulated miRNAs: hsa-miR-4741, hsa-miR-3158-5p, hsa-miR-508-5p, and 57 down-regulated mRNAs, including six hub genes: IGF1, CHEK1, CCNB1, OIP5, BIRC5, AR. GO and KEGG analysis revealed that the network is involved in various biological functions. Immune infiltration analysis showed that IDD was closely related to immune cell infiltration, and hub genes could further affect the development of IDD by affecting immune cell infiltration. Conclusion This study identified the hsa_circ_0074817-hsa-miR-508-5p-IGF1/CHEK1/CCNB1, the hsa_circ_0003600-hsa-miR-4741-BIRC5/OIP5/AR and the hsa_circ_0002702-hsa-miR-3158-5p-IGF1/AR as important regulatory axis of IDD, which will help us gain further insight into the pathogenesis of IDD and determine potential therapeutic targets.
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Affiliation(s)
- Xiaoyang Fang
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Tian Tang
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Daoxi Sun
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shuang Chen
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nan Wang
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lin Xie
- Department of Spine Surgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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Development of a Novel Inflammatory-Associated Gene Signature and Immune Infiltration Patterns in Intervertebral Disc Degeneration. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2481071. [PMID: 36193061 PMCID: PMC9526649 DOI: 10.1155/2022/2481071] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 09/03/2022] [Indexed: 11/17/2022]
Abstract
Background. Both inflammatory factors and immune response play important roles in the pathogenesis of intervertebral disc degeneration (IDD). However, a comprehensive analysis of interaction between inflammatory response-associated genes (IRGs) and immune microenvironment in patients with IDD remains lacking. Hence, the current research is aimed at investigating the correlations between IRG signatures and immune cells in the progression of IDD. Methods. The expression profiles (GSE27494 and GSE41883) and IRGs were downloaded from the Gene Expression Omnibus (GEO) database and Molecular Signature Database (MSigDB), respectively. Weighted gene coexpression network analysis (WGCNA) and differential expression analysis were used to identify the pivotal modules and common differentially expressed genes (DEGs) associated with IDD. Subsequently, we retrieved differentially expressed IRGs (DE-IRGs) by intersecting IRGs and DEGs for enrichment analysis. Next, LASSO regression analyses were performed to screen optimal marker genes for IDD prediction. Additionally, we validated differences DE-IRGs between IDD patients and controls in GSE150408. Finally, the infiltration alteration of immune cells was evaluated by the CIBERSORT, and the correlation between diagnostic markers and infiltrating immune cells was analyzed. Results. A total of 10 upregulated differentially expressed inflammatory genes were identified that were obviously related to progression of IDD. Functional analysis results revealed that DE-IRGs were mainly enriched in signaling pathways TNF, IL-17, NOD-like receptor, and NF-kappa B pathway. A five-gene signature that consisted of IL-1β, LIF, LYN, NAMPT, and SLC7A2 was constructed by the LASSO Cox regression. IL1B, LYN, and NAMPT were further validated as optimal candidate genes in the pathophysiology of IDD. In addition, there was a remarkable immune cell infiltration difference between the healthy and IDD groups. The proportions for dendritic cells activated, mast cells activated, and neutrophils in the IDD group were significantly higher than those in the normal group, while the proportion of some cells was lower than that of the normal group, such as T cell CD4 memory resting, NK cells activated, and macrophage M0. Furthermore, correlation analysis indicated IL-1β, LYN, and NAMPT were closely implicated with immune cell infiltration in IDD development. Conclusions. We explored an association between inflammatory response-associated signature and immune infiltration in IDD and validated that IL-1β, LYN, and NAMPT might serve as biomarkers and therapeutic targets for IDD in the future.
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Development and Validation of a Novel Nomogram to Predict the Risk of Intervertebral Disc Degeneration. Mediators Inflamm 2022; 2022:3665934. [PMID: 36123994 PMCID: PMC9482533 DOI: 10.1155/2022/3665934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
Intervertebral disc degeneration (IVDD) has been a complex disorder resulted from genetic and environmental risk factors. The aim of this study was to identify the risk factors associated with IVDD in orthopaedic patients and develop a prediction model for predicting the risk of IVDD. A total of 309 patients were retrospectively included in the study and randomly divided into the training group and the validation group. The least absolute shrinkage and selection operator regression (LASSO) and the univariate logistic regression analysis were used to optimize factors selection for the IVDD risk model. Multivariable logistic regression analysis was used to establish a predicting nomogram model incorporating the factors. In addition, discrimination, calibration, and clinical usefulness of the nomogram model were evaluated via the C-index, receiver operating characteristic (ROC) curve, calibration plot, and decision curve analysis (DCA). Then, based on the results above, the relationship between IVDD and angiotensin II (AngII) level in peripheral blood was examined prospectively. The predictors of the nomogram include age, sex, hypertension, diabetes, gout, working posture, and exercising hours per week. The C-index values of the training and validation groups were 0.916 (95% CI, 0.876-0.956) and 0.949 (95% CI, 0.909-0.989), respectively, which indicated that the model displayed good discrimination. In addition, the area under the curve (AUC) values of the ROC curve of the training and the validation group were 0.815 (95% CI, 0.759-0.870) and 0.805 (95% CI, 0.718-0.892), respectively, revealing the satisfactory discrimination performance of the model. The prospective investigation showed that the average AngII level in the degenerated group (97.62 ± 44.02 pg/mL) was significantly higher than that in the nondegenerated group (52.91 ± 9.01 pg/mL) (p < 0.001). This present study explored the risk factors for IVDD and established a prediction model, which would effectively predict the risk of IVDD. In addition, based on the prediction model, AngII was revealed to be a potentially auxiliary clinical diagnostic marker for IVDD.
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Li Y, Tian R, Liu J, Li J, Tan H, Wu Q, Fu X. Deciphering the immune landscape dominated by cancer-associated fibroblasts to investigate their potential in indicating prognosis and guiding therapeutic regimens in high grade serous ovarian carcinoma. Front Immunol 2022; 13:940801. [PMID: 36119108 PMCID: PMC9478207 DOI: 10.3389/fimmu.2022.940801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
Limited immunotherapeutic effect in high-grade serous ovarian carcinoma (HGSOC) propels exploration of the mechanics behind this resistance, which may be partly elucidated by investigating characters of cancer-associated fibroblasts (CAFs), a significant population in HGSOC involved in shaping tumor immune microenvironment. Herein, leveraging gene expression data of HGSOC samples from The Cancer Genome Atlas and Gene Expression Omnibus datasets, we suggested that CAFs detrimentally affected the outcomes of HGSOC patients. Subsequently, we performed weighted gene co-expression network analysis (WGCNA) to identify a CAFs-related module and screened out seven hub genes from this module, all of which were positively correlated with the infiltration of immunosuppressive macrophages. As one of the hub genes, the expression of fibrillin 1 (FBN1) and its relevance to CD206 were further verified by immunohistochemistry staining in HGSOC samples. Meanwhile, we extracted genes that correlated well with CAF signatures to construct a CAFscore. The capacity of the CAFscore as an independent prognostic factor was validated by Cox regression analyses, and its relevance to components as well as signals in the tumor immune microenvironment was also investigated. Under the evaluation by the CAFscore, HGSOC patients with relatively high CAFscore had worse outcomes, activated mesenchymal signaling pathways, and immune checkpoint blockade (ICB) resistance signatures, which was consistent with the fact that non-responders in anti-PD-1 treatment cohorts tended to have higher CAFscore. Besides, the possibility of CAFscore to guide the selection of sensitive chemotherapeutic agents was explored. In conclusion, individualized assessment of the CAFscore could uncover the extent of stroma activation and immunosuppression and inform therapeutic strategies to improve the benefit of therapies.
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Affiliation(s)
- Yimin Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruotong Tian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaxin Liu
- Department of Pathology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Hong Tan
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Qihui Wu, ; Hong Tan,
| | - Qihui Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Qihui Wu, ; Hong Tan,
| | - Xiaodan Fu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- *Correspondence: Xiaodan Fu, ; ; Qihui Wu, ; Hong Tan,
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Significance of Immune-Related Genes in the Diagnosis and Classification of Intervertebral Disc Degeneration. J Immunol Res 2022; 2022:2616260. [PMID: 36081453 PMCID: PMC9448583 DOI: 10.1155/2022/2616260] [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: 07/17/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background With the extensive development of intervertebral disc degeneration (IDD) research, IDD has been found to be a complex disease associated with immune-related gene (IRGs) changes. Nonetheless, the roles of IRGs in IDD are unclear. Methods In our study, 11 IRGs were chosen using differential analysis between nondisc degeneration and degenerative patients from the GEO database. Then, we utilized a random forest (RF) model to screen six candidate IRGs to predict the risk of IDD. A nomogram was developed on the basis of six candidate IRGs, and DCA showed that patients could benefit from the nomogram. Based on the selected significant IRGs, a consensus clustering approach was used to differentiate disc degeneration patients into two immune patterns (immune cluster A and B). The PCA algorithm was constructed to compute immune scores for every sample, to quantify immune patterns. The immune scores of immune cluster B patients were higher than those of immune cluster A. Results Through differential expression analysis between healthy and IDD samples, 11 significant IRGs (CTSS, S100Z, STAT3, KLRK1, FPR1, C5AR2, RLN1, IFGR2, IL2RB, IL17RA, and IL6R) were recognized through significant IRGs. The “Reverse Cumulative Distribution of Residual” and “Boxplots of Residual” indicate that the RF model has minimal residuals. The majority of samples in the model have relatively small residuals, demonstrating that the model is better. Besides, the nomogram model was constructed based on importance and the IRGs with importance scores greater than 2 (FPR1, RLN1, S100Z, IFNGR2, KLRK1, and CTSS). The nomogram model revealed that decision-making based on an established model might be beneficial for IDD patients, and the predictive power of the nomogram model was significant. In addition, we identified two different immune cluster patterns (immune cluster A and immune cluster B) based on the 11 IRGs. We found that immune cluster A had significantly higher levels of MDSC, neutrophil, plasmacytoid dendritic cell, and type 17 T helper cell expression than immune cluster B. And we calculated the score for each sample to quantify the gene patterns. The patients in immune cluster B or gene cluster B had higher immune scores than those in immune cluster A or gene cluster A. Conclusion In conclusion, IRGs play an extremely significant role in the occurrence of IDD. Our study of immune patterns may guide the strategies of prevention and treatment for IDD in the future.
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Jiang X, Wu J, Guo C, Song W. Key LncRNAs Associated With Oxidative Stress Were Identified by GEO Database Data and Whole Blood Analysis of Intervertebral Disc Degeneration Patients. Front Genet 2022; 13:929843. [PMID: 35937989 PMCID: PMC9353269 DOI: 10.3389/fgene.2022.929843] [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: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Intervertebral disc degeneration (IDD) is a major cause of low back pain, but the onset and progression of IDD are unknown. Long non-coding RNA (lncRNA) has been validated to play a critical role in IDD, while an increasing number of studies have linked oxidative stress (OS) to the initiation and progression of IDD. We aim to investigate key lncRNAs in IDD through a comprehensive network of competing endogenous RNA (ceRNA) and to identify possible underlying mechanisms. Methods: We downloaded IDD-related gene expression data from the Gene Expression Omnibus (GEO) database and obtained differentially expressed-lncRNAs (DE-lncRNA), -microRNAs (DE-miRNA), and -messenger RNAs (DE-mRNA) by bioinformatics analysis. The OS-related lncRNA-miRNA-mRNA ceRNA interaction axis was constructed and key lncRNAs were identified based on ceRNA theory. We performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses on mRNAs regulated by lncRNAs in the ceRNA network. Single sample gene set enrichment analysis (ssGSEA) was used to reveal the immune landscape. Expression of key lncRNAs in IDD was assessed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Results: In this study, 111 DE-mRNAs, 20 DE-lncRNAs, and 502 DE-miRNAs were identified between IDD patients and controls, and 16 OS-related DE-lncRNAs were also identified. The resulting lncRNA-miRNA-mRNA network consisted of eight OS-related DE-lncRNA nodes, 24 DE-miRNA nodes, 70 DE-mRNA nodes, and 183 edges. Functional enrichment analysis suggested that the ceRNA network may be involved in regulating biological processes related to cytokine secretion, lipid, and angiogenesis. We also identified four key lncRNAs, namely lncRNA GNAS-AS1, lncRNA MIR100HG, lncRNA LINC01359, and lncRNA LUCAT1, which were also found to be significantly associated with immune cells. Conclusion: These results provide novel insights into the potential applications of OS-related lncRNAs in patients with IDD.
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Li W, Zhang S, Zhao Y, Wang D, Shi Q, Ding Z, Wang Y, Gao B, Yan M. Revealing the Key MSCs Niches and Pathogenic Genes in Influencing CEP Homeostasis: A Conjoint Analysis of Single-Cell and WGCNA. Front Immunol 2022; 13:933721. [PMID: 35833124 PMCID: PMC9271696 DOI: 10.3389/fimmu.2022.933721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/30/2022] [Indexed: 01/24/2023] Open
Abstract
Degenerative disc disease (DDD), a major contributor to discogenic pain, which is mainly resulted from the dysfunction of nucleus pulposus (NP), annulus fibrosis (AF) and cartilage endplate (CEP) cells. Genetic and cellular components alterations in CEP may influence disc homeostasis, while few single-cell RNA sequencing (scRNA-seq) report in CEP makes it a challenge to evaluate cellular heterogeneity in CEP. Here, this study conducted a first conjoint analysis of weighted gene co-expression network analysis (WGCNA) and scRNA-seq in CEP, systematically analyzed the interested module, immune infiltration situation, and cell niches in CEP. WGCNA and protein-protein interaction (PPI) network determined a group of gene signatures responsible for degenerative CEP, including BRD4, RAF1, ANGPT1, CHD7 and NOP56; differentially immune analysis elucidated that CD4+ T cells, NK cells and dendritic cells were highly activated in degenerative CEP; then single-cell resolution transcriptomic landscape further identified several mesenchymal stem cells and other cellular components focused on human CEP, which illuminated niche atlas of different cell subpopulations: 8 populations were identified by distinct molecular signatures. Among which, NP progenitor/mesenchymal stem cells (NPMSC), also served as multipotent stem cells in CEP, exhibited regenerative and therapeutic potentials in promoting bone repair and maintaining bone homeostasis through SPP1, NRP1-related cascade reactions; regulatory and effector mesenchymal chondrocytes could be further classified into 2 different subtypes, and each subtype behaved potential opposite effects in maintaining cartilage homeostasis; next, the potential functional differences of each mesenchymal stem cell populations and the possible interactions with different cell types analysis revealed that JAG1, SPP1, MIF and PDGF etc. generated by different cells could regulate the CEP homeostasis by bone formation or angiogenesis, which could be served as novel therapeutic targets for degenerative CEP. In brief, this study mainly revealed the mesenchymal stem cells populations complexity and phenotypic characteristics in CEP. In brief, this study filled the gap in the knowledge of CEP components, further enhanced researchers’ understanding of CEP and their cell niches constitution.
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Affiliation(s)
- Weihang Li
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Shilei Zhang
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Yingjing Zhao
- Department of Intensive Care Unit, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Dong Wang
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- Department of Orthopaedics, Affiliated Hospital of Yanan University, Yanan, China
| | - Quan Shi
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- Department of Orthopaedics, Affiliated Hospital of Yanan University, Yanan, China
| | - Ziyi Ding
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Yongchun Wang
- Department of Aerospace Medical Training, School of Aerospace Medicine, Air Force Medical University, Xi’an, China
- Key Lab of Aerospace Medicine, Chinese Ministry of Education, Xi’an, China
- *Correspondence: Ming Yan, ; Bo Gao, ; Yongchun Wang,
| | - Bo Gao
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Ming Yan, ; Bo Gao, ; Yongchun Wang,
| | - Ming Yan
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Ming Yan, ; Bo Gao, ; Yongchun Wang,
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Identification of SMIM1 and SEZ6L2 as Potential Biomarkers for Genes Associated with Intervertebral Disc Degeneration in Pyroptosis. DISEASE MARKERS 2022; 2022:9515571. [PMID: 35578687 PMCID: PMC9107366 DOI: 10.1155/2022/9515571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
Abstract
Background. Inflammatory reactions and pyroptosis play an important role in the pathology of intervertebral disc degeneration (IDD). The aim of the present study was to investigate pyroptosis in the nucleus pulposus cells (NPCs) of inflammatory induced IDD by bioinformatic methods and to search for possible diagnostic biomarkers. Methods. Gene expression profiles related to IDD were downloaded from the GEO database to identify differentially expressed genes (DEGs) between inflammation-induced IDD and non-inflammatory intervention samples. Pyroptosis genes were then searched for, and their expression in IDD was analyzed. Weighted gene co-expression network analysis (WGCNA) was then used to search for modules of IDD genes associated with pyroptosis and intersected with DEGs to discover candidate genes that would be diagnostically valuable. A LASSO model was developed to screen for genes that met the requirements, and ROC curves were created to clarify the diagnostic value of the genetic markers. Ultimately, the screened genes were further validated, and their diagnostic value assessed by selecting gene sets from the GEO database. RT-PCR was used to assess the mRNA expression of diagnostic markers in the nucleus pulposus (NP). Pan-cancer analysis was applied to demonstrate the expression and prognostic value of the screened genes in various tumors. Results. A total of 733 DEGs were identified in GSE41883 and GSE27494, which were mainly enriched in transmembrane receptor protein serine/threonine, kinase signaling pathway, response to lipopolysaccharide, and other biological processes, and they were mainly related to TGF beta signaling pathway, toll-like receptor signaling pathway, and TNF signaling pathway. A total of 81 genes related to pyroptosis were identified in the literature, and eight genes related to IDD were identified in the Veen diagram, namely, IL1A, IL1B, NOD2, GBP1, IL6, AK1, EEF2K, and PYCARD. Eleven candidate genes were obtained after locating the intersection of pyroptosis-related module genes and DEGs according to WGCNA analysis. A total of six valid genes were obtained after constructing a machine learning model, and five key genes were finally identified after correlation analysis. GSE23132 and GSE56081 validated the candidate genes, and the final IDD-related diagnostic markers were obtained as SMIM1 and SEZ6L2. RT-PCR results indicated that the mRNA expression of both was significantly elevated in IDD. The pan-cancer analysis demonstrated that SMIM1 and SEZ6L2 have important roles in the expression and prognosis of various tumors. Conclusion. In conclusion, this research identifies SMIM1 and SEZ6L2 as important biomarkers of IDD associated with pyroptosis, which will help to unravel the development and pathogenesis of IDD and determine potential therapeutic targets.
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Zhao Y, Li W, Zhang K, Xu M, Zou Y, Qiu X, Lu T, Gao B. Revealing oxidative stress-related genes in osteoporosis and advanced structural biological study for novel natural material discovery regarding MAPKAPK2. Front Endocrinol (Lausanne) 2022; 13:1052721. [PMID: 36479222 PMCID: PMC9720258 DOI: 10.3389/fendo.2022.1052721] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES This study aimed to find novel oxidative stress (OS)-related biomarkers of osteoporosis (OP), together with targeting the macromolecule Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) protein to further discover potential novel materials based on an advanced structural biology approach. METHODS Gene expression profiles of GSE35958 were obtained from the Gene Expression Omnibus (GEO) database, which were included for weighted gene co-expression network analysis (WGCNA) and differential analysis to identify the most correlated module, to identify OS-related hub genes in the progression of OP. Functional annotations were also analyzed on the interested module to get a comprehensive understanding of these genes. Then, a series of advanced structural biology methods, including high-throughput screening, pharmacological characteristic prediction, precise molecular docking, molecular dynamics simulation, etc., was implemented to discover novel natural inhibitor materials against the MAPKAPK2 protein. RESULTS The brown module containing 720 genes was identified as the interested module, and a group set of genes was determined as the hub OS-related genes, including PPP1R15A, CYB5R3, BCL2L1, ABCD1, MAPKAPK2, HSP90AB1, CSF1, RELA, P4HB, AKT1, HSP90B1, and CTNNB1. Functional analysis demonstrated that these genes were primarily enriched in response to chemical stress and several OS-related functions. Then, Novel Materials Discovery demonstrated that two compounds, ZINC000014951634 and ZINC000040976869, were found binding to MAPKAPK2 with a favorable interaction energy together with a high binding affinity, relatively low hepatoxicity and carcinogenicity, high aqueous solubility and intestinal absorption levels, etc., indicating that the two compounds were ideal potential inhibitor materials targeting MAPKAPK2. CONCLUSION This study found a group set of OS-related biomarkers of OP, providing further insights for OS functions in the development of OP. This study then focused on one of the macromolecules, MAPKAPK2, to further discover potential novel materials, which was of great significance in guiding the screening of MAPKAPK2 potential materials.
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Affiliation(s)
- Yingjing Zhao
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weihang Li
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
| | - Kuo Zhang
- State Key Laboratory of Cancer Biology, Biotechnology Center, School of Pharmacy, Fourth Military Medical University, Xi’an, China
| | - Meng Xu
- Department of Aerospace Medical Training, School of Aerospace Medicine, Air Force Medical University, Xi’an, China
- Key Lab of Aerospace Medicine, Chinese Ministry of Education, Xi’an, China
| | - Yujia Zou
- College of Clinical Medicine, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaotong Qiu
- Department of Hepatic Surgery and Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Liver Disease Research, Guangdong Engineering Laboratory for Transplantation, Guangzhou, China
| | - Tianxing Lu
- Zonglian College, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Bo Gao
- Department of Orthopedic Surgery, Xijing Hospital, Air Force Medical University, Xi’an, China
- *Correspondence: Bo Gao,
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