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Chen S, Ye J, Lin Y, Chen W, Huang S, Yang Q, Qian H, Gao S, Hua C. Crucial Roles of RSAD2/viperin in Immunomodulation, Mitochondrial Metabolism and Autoimmune Diseases. Inflammation 2024:10.1007/s10753-024-02076-5. [PMID: 38909344 DOI: 10.1007/s10753-024-02076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Autoimmune diseases are typically characterized by aberrant activation of immune system that leads to excessive inflammatory reactions and tissue damage. Nevertheless, precise targeted and efficient therapies are limited. Thus, studies into novel therapeutic targets for the management of autoimmune diseases are urgently needed. Radical S-adenosyl methionine domain-containing 2 (RSAD2) is an interferon-stimulated gene (ISG) renowned for the antiviral properties of the protein it encodes, named viperin. An increasing number of studies have underscored the new roles of RSAD2/viperin in immunomodulation and mitochondrial metabolism. Previous studies have shown that there is a complex interplay between RSAD2/vipeirn and mitochondria and that binding of the iron-sulfur (Fe-S) cluster is necessary for the involvement of viperin in mitochondrial metabolism. Viperin influences the proliferation and development of immune cells as well as inflammation via different signaling pathways. However, the function of RSAD2/viperin varies in different studies and a comprehensive overview of this emerging theme is lacking. This review will describe the characteristics of RSAD2/viperin, decipher its function in immunometabolic processes, and clarify the crosstalk between RSAD2/viperin and mitochondria. Furthermore, we emphasize the crucial roles of RSAD2 in autoimmune diseases and its potential application value.
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Affiliation(s)
- Siyan Chen
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Jiani Ye
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Yinfang Lin
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Wenxiu Chen
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Shenghao Huang
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Qianru Yang
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Hengrong Qian
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Sheng Gao
- Laboratory Animal Center, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China.
| | - Chunyan Hua
- School of Basic Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China.
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Veyssiere M, Rodriguez Ordonez MDP, Chalabi S, Michou L, Cornelis F, Boland A, Olaso R, Deleuze JF, Petit-Teixeira E, Chaudru V. MYLK* FLNB and DOCK1* LAMA2 gene-gene interactions associated with rheumatoid arthritis in the focal adhesion pathway. Front Genet 2024; 15:1375036. [PMID: 38803542 PMCID: PMC11128622 DOI: 10.3389/fgene.2024.1375036] [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: 01/23/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease caused by a combination of genetic and environmental factors. Rare variants with low predicted effects in genes participating in the same biological function might be involved in developing complex diseases such as RA. From whole-exome sequencing (WES) data, we identified genes containing rare non-neutral variants with complete penetrance and no phenocopy in at least one of nine French multiplex families. Further enrichment analysis highlighted focal adhesion as the most significant pathway. We then tested if interactions between the genes participating in this function would increase or decrease the risk of developing RA disease. The model-based multifactor dimensionality reduction (MB-MDR) approach was used to detect epistasis in a discovery sample (19 RA cases and 11 healthy individuals from 9 families and 98 unrelated CEU controls from the International Genome Sample Resource). We identified 9 significant interactions involving 11 genes (MYLK, FLNB, DOCK1, LAMA2, RELN, PIP5K1C, TNC, PRKCA, VEGFB, ITGB5, and FLT1). One interaction (MYLK*FLNB) increasing RA risk and one interaction decreasing RA risk (DOCK1*LAMA2) were confirmed in a replication sample (200 unrelated RA cases and 91 GBR unrelated controls). Functional and genomic data in RA samples or relevant cell types argue the key role of these genes in RA.
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Affiliation(s)
- Maëva Veyssiere
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
| | | | - Smahane Chalabi
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
| | - Laetitia Michou
- Division of Rheumatology, Department of Medicine, CHU de Québec-Université Laval, Québec City, QC, Canada
| | - François Cornelis
- Génétiqe-Oncogénétique Adulte-Prévention, Institut National de la Santé et de la Recherche Médicale, Clermont-Auvergne University and CHU, Clermont-Ferrand, France
| | - Anne Boland
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Commissariat à l'Energie Atomique, Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, Evry, France
| | | | - Valérie Chaudru
- Institut National de la Santé et de la Recherche Médicale, Université de Paris, Paris, France
- GenHotel—Univ Evry, University of Paris Saclay, Evry, France
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Wu Y, Chen W, Jian J, Liu W, Wang H, Gao D, Liu W. The potential molecular markers of inflammatory response in KOA with AD based on single-cell transcriptome sequencing analysis and identification of ligands by virtual screening. Mol Divers 2024:10.1007/s11030-024-10854-4. [PMID: 38622351 DOI: 10.1007/s11030-024-10854-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 03/20/2024] [Indexed: 04/17/2024]
Abstract
Alzheimer's disease (AD) and osteoarthritis (OA) are both senile degenerative diseases. Clinical studies have found that OA patients have a significantly increased risk of AD in their later life. This study hypothesized that chronic aseptic inflammation might lead to AD in KOA patients. However, current research has not yet clarified the potential mechanism between AD and KOA. Therefore, this study intends to use KOA transcriptional profiling and single-cell sequencing analysis technology to explore the molecular mechanism of KOA affecting AD development, and screen potential molecular biomarkers and drugs for the prediction, diagnosis, and prognosis of AD in KOA patients. It was found that the higher the expression of TXNIP, MMP3, and MMP13, the higher the risk coefficient of AD was. In addition, the AUC of TXNIP, MMP3, and MMP13 were all greater than 0.70, which had good diagnostic significance for AD. Finally, through the virtual screening of core proteins in FDA drugs and molecular dynamics simulation, it was found that compound Cobicistat could be targeted to TXNIP, Itc could be targeted to MMP3, and Isavuconazonium could be targeted to MMP13. To sum up, TXNIP, MMP3, and MMP13 are prospective molecular markers in KOA with AD, which could be used to predict, diagnose, and prognosis.
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Affiliation(s)
- Yufeng Wu
- Traditional Chinese Medicine Hospital of Zhongshan, Zhongshan, 528400, Guangdong, China
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Weijian Chen
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
- The Fifth Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510095, China
- Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, 510095, China
| | - Junde Jian
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
- Guangzhou Orthopedic Hospital, Guangdong Province, Guangzhou University of Chinese Medicine, Guangzhou, 510045, China
| | - Weinian Liu
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
- Guangzhou Orthopedic Hospital, Guangdong Province, Guangzhou University of Chinese Medicine, Guangzhou, 510045, China
| | - Haibin Wang
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
- The First Clinical Medical College, Guangdong Province, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Dawei Gao
- Traditional Chinese Medicine Hospital of Zhongshan, Zhongshan, 528400, Guangdong, China
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China
| | - Wengang Liu
- Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, China.
- The Fifth Clinical College of Guangzhou, University of Chinese Medicine, Guangzhou, 510095, China.
- Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, 510095, China.
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Liu T, Li X, Pang M, Wang L, Li Y, Sun X. Machine learning-based endoplasmic reticulum-related diagnostic biomarker and immune microenvironment landscape for osteoarthritis. Aging (Albany NY) 2024; 16:4563-4578. [PMID: 38428406 PMCID: PMC10968715 DOI: 10.18632/aging.205611] [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: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Osteoarthritis (OA) is the most common degenerative joint disease worldwide. Further improving the current limited understanding of osteoarthritis has positive clinical value. METHODS OA samples were collected from GEO database and endoplasmic reticulum related genes (ERRGs) were identified. The WGCNA network was further built to identify the crucial gene module. Based on the expression profiles of characteristic ERRGs, LASSO algorithm was used to select key factors according to the minimum λ value. Random forest (RF) algorithm was used to calculate the importance of ERRGs. Subsequently, overlapping genes based on LASSO and RF algorithms were identified as ERRGs-related diagnostic biomarkers. In addition, OA specimens were also collected and performed qRT-PCR quantitative analysis of selected ERRGs. RESULTS We identified four ERRGs associated with OA risk assessment through machine learning methods, and verified the abnormal expressions of these screened markers in OA patients through in vitro experiments. The influence of selected markers on OA immune infiltration was also evaluated. CONCLUSIONS Our results provide new evidence for the role of ER stress in the OA progression, as well as new markers and potential intervention targets for OA.
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Affiliation(s)
- Tingting Liu
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
| | - Xiaomao Li
- Jiangsu Food and Pharmaceutical Science College, Huaian, Jiangsu 223023, China
| | - Mu Pang
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine (Shenzhen Traditional Chinese Medicine Hospital), Shenzhen, Guangdong 518000, China
| | - Lifen Wang
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
| | - Ye Li
- Chongqing Three Gorges Medical College, Chongqing 404120, China
| | - Xizhe Sun
- Research Center for Drug Safety Evaluation of Hainan, Hainan Medical University, Haikou, Hainan 571199, China
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Zhan H, Cheng L, Li H, Liu Y, Huang Y, Li X, Yan S, Li Y. Integrated analyses delineate distinctive immunological pathways and diagnostic signatures for Behcet's disease by leveraging gene microarray data. Immunol Res 2023; 71:860-872. [PMID: 37341899 DOI: 10.1007/s12026-023-09398-w] [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: 08/01/2022] [Accepted: 05/22/2023] [Indexed: 06/22/2023]
Abstract
Behcet's disease (BD) is a chronic inflammatory vasculitis and clinically heterogeneous disorder caused by immunocyte aberrations. Comprehensive research on gene expression patterns in BD illuminating its aetiology is lacking. E-MTAB-2713 downloaded from ArrayExpress was analysed to screen differentially expressed genes (DEGs) using limma. Random forest (RF) and neural network (NN) classification models composed of gene signatures were established using the E-MTAB-2713 training set and subsequently verified using GSE17114. Single sample gene set enrichment analysis was used to assess immunocyte infiltration. After identifying DEGs in E-MTAB-2713, pathogen-triggered, lymphocyte-mediated and angiogenesis- and glycosylation-related inflammatory pathways were discovered to be predominant in BD episodes. Gene signatures from the RF and NN diagnostic models, together with genes enriched in angiogenesis and glycosylation pathways, well discriminated the clinical subtypes of BD manifesting as mucocutaneous, ocular and large vein thrombosis involvement in GSE17114. Moreover, a distinctive immunocyte profile revealed T, NK and dendritic cell activation in BD compared to the findings in healthy controls. Our findings suggested that EPHX1, PKP2, EIF4B and HORMAD1 expression in CD14+ monocytes and CSTF3 and TCEANC2 expression in CD16+ neutrophils could serve as combined gene signatures for BD phenotype differentiation. Pathway genes comprising ATP2B4, MYOF and NRP1 for angiogenesis and GXYLT1, ENG, CD69, GAA, SIGLEC7, SIGLEC9 and SIGLEC16 for glycosylation also might be applicable diagnostic markers for subtype identification.
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Affiliation(s)
- Haoting Zhan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yongmei Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yuan Huang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Xiaomeng Li
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Songxin Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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Zhao J, Duan X, Yan S, Liu Y, Wang K, Hu M, Chai Q, Liu L, Ge C, Jia J, Dou T. Transcriptomics reveals the molecular regulation of Chinese medicine formula on improving bone quality in broiler. Poult Sci 2023; 102:103044. [PMID: 37717480 PMCID: PMC10507442 DOI: 10.1016/j.psj.2023.103044] [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: 05/19/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Skeletal disorder is of concern to the poultry industry as it affects animal welfare and production performance. Traditional Chinese medicine could improve bone quality and reduce the incidence of bone disease, but the molecular regulation of Chinese medicine formula (CMF) on improving bone quality in broilers is still unclear. This study was performed to research the effects of CMF on skeletal performance of Cobb broilers and reveal the molecular regulation. A total of 120 one-day-old Cobb broilers were randomly allocated into 4 equal groups of 30 chickens, with 5 replicates and 6 chickens in each replicate. The control (CON) group was fed a diet without CMF, while the CMF1, CMF2, and CMF3 groups were supplemented with different CMF at 6,000 mg/kg diet, respectively. The broilers were raised to 60 d of age, then bone tissues were collected for biomechanical properties, micro-CT detection and transcriptomic sequencing analysis. The results showed that CMF3 improved the biomechanical properties of broiler tibia, via increasing the elastic modulus (P < 0.05), yield strength (P > 0.05), maximum stress (P < 0.05) and fracture stress (P < 0.05) of the tibia. Micro-CT analysis indicated that CMF3 increased the bone mineral density (BMD), bone volume/total volume (BV/TV), bone surface density (BS/TV), trabecular number (Tb.N), trabecular thickness (Tb.Th), and decreased the trabecular separation (Tb.Sp) of femur cancellous bone (P < 0.05). RNA-seq analysis revealed 2,177 differentially expressed genes (DEGs) (|log2FoldChange| ≥ 1, FDR < 0.05) between the CMF3 group and CON group. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis showed 13 pathways mostly associated with bone growth and development and bone metabolism, and we identified 39 bone-related DEGs. This study suggests that CMF3 could improve bone strength and bone microstructure of broilers, and showed a positive effect on bone performance. Our research could provide a theoretical reference for the development of pollution-free feed additives to improve the skeletal performance of broilers, which could help promote healthy farming of chickens.
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Affiliation(s)
- Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Xiaohua Duan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China; Yunnan University of Chinese Medicine, 650500 Kunming, China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Mei Hu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Qian Chai
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China; Yunnan Vocational and Technical College of Agriculture, 650031 Kunming, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China.
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Rocchetti MT, Bizzoca D, Moretti L, Ragni E, Moretti FL, Vicenti G, Solarino G, Rizzello A, Petruzzella V, Palese LL, Scacco S, Banfi G, Moretti B, Gnoni A. A Gel-Based Proteomic Analysis Reveals Synovial α-Enolase and Fibrinogen β-Chain Dysregulation in Knee Osteoarthritis: A Controlled Trial. J Pers Med 2023; 13:916. [PMID: 37373906 PMCID: PMC10305339 DOI: 10.3390/jpm13060916] [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: 04/26/2023] [Revised: 05/28/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND The identification of synovial fluid (SF) biomarkers that could anticipate the diagnosis of osteoarthritis (OA) is gaining increasing importance in orthopaedic clinical practice. This controlled trial aims to assess the differences between the SF proteome of patients affected by severe OA undergoing Total Knee Replacement (TKR) compared to control subjects (i.e., subjects younger than 35, undergoing knee arthroscopy for acute meniscus injury). METHODS The synovial samples were collected from patients with Kellgren Lawrence grade 3 and 4 knee osteoarthritis undergoing THR (study group) and young patients with meniscal tears and no OA signs undergoing arthroscopic surgery (control group). The samples were processed and analyzed following the protocol defined in our previous study. All of the patients underwent clinical evaluation using the International Knee Documentation Committee (IKDC) subjective knee evaluation (main outcome), Knee Society Clinical Rating System (KSS), Knee injury and Osteoarthritis Outcome Score (KOOS), and Visual Analogue Scale (VAS) for pain. The drugs' assumptions and comorbidities were recorded. All patients underwent preoperative serial blood tests, including complete blood count and C-Reactive Protein (CRP). RESULTS The synovial samples' analysis showed a significantly different fibrinogen beta chain (FBG) and alpha-enolase 1 (ENO1) concentration in OA compared to the control samples. A significant correlation between clinical scores, FBG, and ENO1 concentration was observed in osteoarthritic patients. CONCLUSIONS Synovial fluid FBG and ENO1 concentrations are significantly different in patients affected by knee OA compared with non-OA subjects.
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Affiliation(s)
- Maria Teresa Rocchetti
- Department of Clinical and Experimental Medicine, University of Foggia, Via Pinto 1, 71122 Foggia, Italy
| | - Davide Bizzoca
- Orthopaedics Unit-UOSD Vertebral Surgery, DAI Neuroscience, Sense Organs and Locomotor System, AOU Consorziale Policlinico, 70124 Bari, Italy
- PhD Course in Public Health, Clinical Medicine and Oncology, DiMePre-J, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Lorenzo Moretti
- Orthopaedics Unit-UOSD Vertebral Surgery, DAI Neuroscience, Sense Organs and Locomotor System, AOU Consorziale Policlinico, 70124 Bari, Italy
| | - Enrico Ragni
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Via R. Galeazzi 4, 20161 Milano, Italy
| | - Francesco Luca Moretti
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Via R. Galeazzi 4, 20161 Milano, Italy
- National Centre for Chemicals, Cosmetic Products and Consumer Protection, National Institute of Health, 00161 Rome, Italy
| | - Giovanni Vicenti
- Orthopaedics Unit-UOSD Vertebral Surgery, DAI Neuroscience, Sense Organs and Locomotor System, AOU Consorziale Policlinico, 70124 Bari, Italy
| | - Giuseppe Solarino
- Orthopaedics Unit-UOSD Vertebral Surgery, DAI Neuroscience, Sense Organs and Locomotor System, AOU Consorziale Policlinico, 70124 Bari, Italy
| | - Alessandro Rizzello
- Clinical Biochemistry, DiBraiN, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Vittoria Petruzzella
- Clinical Biochemistry, DiBraiN, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Luigi Leonardo Palese
- Clinical Biochemistry, DiBraiN, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Salvatore Scacco
- Clinical Biochemistry, DiBraiN, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Giuseppe Banfi
- IRCCS Galeazzi-Sant'Ambrogio, Via Cristina Belgioioso 173, 20157 Milano, Italy
- Faculty of Medicine, Università Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milano, Italy
| | - Biagio Moretti
- Orthopaedics Unit-UOSD Vertebral Surgery, DAI Neuroscience, Sense Organs and Locomotor System, AOU Consorziale Policlinico, 70124 Bari, Italy
| | - Antonio Gnoni
- Clinical Biochemistry, DiBraiN, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
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Yan Z, Xu J, Wu G, Zhen Y, Liao X, Zou F. Identification of key genes and pathways associated with gender difference in osteonecrosis of the femoral head based on bioinformatics analysis. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2023; 23:122-130. [PMID: 36856107 PMCID: PMC9976184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To identify different key genes and pathways between males and females by studying differentially expressed genes (DEGs). METHODS The gene expression data of GSE123568 were downloaded from GEO database, including osteonecrosis of the femoral head (ONFH) samples from 3 females and 7 males, and DEGs between different gender were identified with R software. Protein-protein interaction (PPI) network was constructed to further analyze the interactions between overlapping DEGs, and finally, GO, KEGG and gene set enrichment analysis (GSEA) were conducted for enrichment analysis. RESULTS 131 DEGs were identified between ONFH females and ONFH males, including 76 up-regulated genes and 55 down-regulated genes. And 10 hub genes were identified in PPI network, including SLC4A1, GYPA, CXCL8, IFIT1, GBP5, IFI44, IFI44L, IFIT3, KEL and AHSP. Functional enrichment analysis revealed that these genes were mainly enriched in cGMP-PKG signaling pathway, Fatty acid degradation, Non-alcoholic fatty liver disease, Systemic lupus erythematosus, Hematopoietic cell lineage and NO-cGMP-PKG signaling. CONCLUSIONS NO-cGMP-PKG signaling may play an important role in the occurrence and development of ONFH. SLC4A1, GYPA, CXCL8, GBP5 and AHSP may be key genes associated with gender difference in the progression of ONFH, which may be ideal targets or prognostic markers for the treatment of ONFH.
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Affiliation(s)
- Zijian Yan
- Department of Orthopeadics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, China
| | - Junchang Xu
- Department of Orthopeadics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, China
| | - Guihua Wu
- Department of General Surgery, Affiliated Hospital of Xiangyang Vocational and Technical College, China
| | - Yongling Zhen
- Department of Orthopeadics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, China
| | - Xiaolong Liao
- Department of Orthopeadics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, China
| | - Feng Zou
- Department of Orthopeadics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, China
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Multiple Genetic Loci Associated with Pug Dog Thoracolumbar Myelopathy. Genes (Basel) 2023; 14:genes14020385. [PMID: 36833311 PMCID: PMC9957375 DOI: 10.3390/genes14020385] [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: 12/21/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Pug dogs with thoracolumbar myelopathy (PDM) present with a specific clinical phenotype that includes progressive pelvic limb ataxia and paresis, commonly accompanied by incontinence. Vertebral column malformations and lesions, excessive scar tissue of the meninges, and central nervous system inflammation have been described. PDM has a late onset and affects more male than female dogs. The breed-specific presentation of the disorder suggests that genetic risk factors are involved in the disease development. To perform a genome-wide search for PDM-associated loci, we applied a Bayesian model adapted for mapping complex traits (BayesR) and a cross-population extended haplotype homozygosity test (XP-EHH) in 51 affected and 38 control pugs. Nineteen associated loci (harboring 67 genes in total, including 34 potential candidate genes) and three candidate regions under selection (with four genes within or next to the signal) were identified. The multiple candidate genes identified have implicated functions in bone homeostasis, fibrotic scar tissue, inflammatory responses, or the formation, regulation, and differentiation of cartilage, suggesting the potential relevance of these processes to the pathogenesis of PDM.
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Wu F, An Y, Zhou L, Zhao Y, Chen L, Wang J, Wu G. Whole-transcriptome sequencing and ceRNA interaction network of temporomandibular joint osteoarthritis. Front Genet 2022; 13:962574. [PMID: 36276964 PMCID: PMC9581126 DOI: 10.3389/fgene.2022.962574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/20/2022] [Indexed: 11/20/2023] Open
Abstract
Purpose: The aim of this study was to conduct a comprehensive transcriptomic analysis to explore the potential biological functions of noncoding RNA (ncRNAs) in temporomandibular joint osteoarthritis (TMJOA). Methods: Whole transcriptome sequencing was performed to identify differentially expressed genes (DEGs) profiles between the TMJOA and normal groups. The functions and pathways of the DEGs were analyzed using Metascape, and a competitive endogenous RNA (ceRNA) network was constructed using Cytoscape software. Results: A total of 137 DEmRNAs, 65 DEmiRNAs, 132 DElncRNAs, and 29 DEcircRNAs were identified between the TMJOA and normal groups. Functional annotation of the DEmRNAs revealed that immune response and apoptosis are closely related to TMJOA and also suggested key signaling pathways related to TMJOA, including chronic depression and PPAR signaling pathways. We identified vital mRNAs, including Klrk1, Adipoq, Cryab, and Hspa1b. Notably, Adipoq expression in cartilage was significantly upregulated in TMJOA compared with normal groups (10-fold, p < 0.001). According to the functional analysis of DEmRNAs regulated by the ceRNA network, we found that ncRNAs are involved in the regulation of autophagy and apoptosis. In addition, significantly DEncRNAs (lncRNA-COX7A1, lncRNA-CHTOP, lncRNA-UFM1, ciRNA166 and circRNA1531) were verified, and among these, circRNA1531 (14.5-fold, p < 0.001) and lncRNA-CHTOP (14.8-fold, p < 0.001) were the most significantly downregulated ncRNAs. Conclusion: This study showed the potential of lncRNAs, circRNAs, miRNAs, and mRNAs may as clinical biomarkers and provides transcriptomic insights into their functional roles in TMJOA. This study identified the transcriptomic signatures of mRNAs associated with immunity and apoptosis and the signatures of ncRNAs associated with autophagy and apoptosis and provides insight into ncRNAs in TMJOA.
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Affiliation(s)
- Fan Wu
- School of Basic Medicine, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China
- Department of Implantology, School of Stomatology, National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, Fourth Military Medical University, Xi’an, China
| | - Yanxin An
- Department of General Surgery, The First Affiliated Hospital of Xi’an Medical University, Xi’an, China
| | - Libo Zhou
- School of Basic Medicine, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China
| | - Yuqing Zhao
- School of Stomatology, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China
| | - Lei Chen
- Department of Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong University, Jinan, China
| | - Jing Wang
- Department of Implantology, School of Stomatology, National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, Fourth Military Medical University, Xi’an, China
| | - Gaoyi Wu
- School of Basic Medicine, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China
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11
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Du Y, Cui R, Tian N, Chen M, Zhang XL, Dai SM. Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway. Arthritis Res Ther 2022; 24:188. [PMID: 35941675 PMCID: PMC9358906 DOI: 10.1186/s13075-022-02880-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background The upregulation of interferon (IFN)-stimulated genes induced by type I IFNs (namely type I IFN signature) in rheumatoid arthritis (RA) patients had implications in early diagnosis and prediction of therapy responses. However, factors that modulate the type I IFN signature in RA are largely unknown. In this study, we aim to explore the involvement of VGLL3, a homologue of the vestigial-like gene in Drosophila and a putative regulator of the Hippo pathway, in the modulation of type I IFN signature in the fibroblast-like synoviocytes (FLS) of RA patients. Methods FLS were isolated from RA and osteoarthritis (OA) patients. Expression of VGLL3 in the synovial tissues and FLS was analyzed by immunohistochemistry and PCR. RNA sequencing was performed in RA-FLS upon VGLL3 overexpression. The expression of IFN-stimulated genes was examined by PCR and Western blotting. Results VGLL3 was upregulated in the RA synovium and RA-FLS compared to OA. Overexpression of VGLL3 promoted the expression of IFN-stimulated genes in RA-FLS. The expression of STAT1 and MX1 was also upregulated in RA synovium compared to OA and was associated with the expression of VGLL3 in RA and OA patients. VGLL3 promoted the IRF3 activation and IFN-β1 expression in RA-FLS. Increased IFN-β1 induced the expression of IFN-stimulated genes in RA-FLS in an autocrine manner. VGLL3 also modulated the expression of the Hippo pathway molecules WWTR1 and AMOTL2, which mediated the regulation of IRF3 activation and IFN-β1 production by VGLL3 in RA-FLS. Conclusions VGLL3 drives the IRF3-induced IFN-β1 expression in RA-FLS by inhibiting WWTR1 expression and subsequently promotes the type I IFN signature expression in RA-FLS through autocrine IFN-β1 signaling.
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Affiliation(s)
- Yu Du
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Ran Cui
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Na Tian
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Miao Chen
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China
| | - Xian-Long Zhang
- Department of Orthopedic Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Sheng-Ming Dai
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yishan Road, Shanghai, 200233, China.
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12
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Genetic association and single-cell transcriptome analyses reveal distinct features connecting autoimmunity with cancers. iScience 2022; 25:104631. [PMID: 35800769 PMCID: PMC9254016 DOI: 10.1016/j.isci.2022.104631] [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: 02/17/2022] [Revised: 05/08/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Autoimmune diseases (ADs) are at a significantly higher risk of cancers with unclear mechanism. By searching GWAS catalog database and Medline, susceptible genes for five common ADs, including systemic lupus erythematosus (SLE), rheumatoid arthritis, Sjögren syndrome, systemic sclerosis, and idiopathic inflammatory myopathies, were collected and then were overlapped with cancer driver genes. Single-cell transcriptome analysis was performed in the comparation between SLE and related cancer. We identified 45 carcinogenic autoimmune disease risk (CAD) genes, which were mainly enriched in T cell signaling pathway and B cell signaling pathway. Integrated single-cell analysis revealed immune cell signaling was significantly downregulated in renal cancer compared with SLE, while stemness signature was significantly enriched in both renal cancer or lymphoma and SLE in specific subpopulations. Drugs targeting CAD genes were shared between ADs and cancer. Our study highlights the common and specific features between ADs and related cancers, and sheds light on a new discovery of treatments.
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13
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Zhou J, Zou D, Wan R, Liu J, Zhou Q, Zhou Z, Wang W, Tao C, Liu T. Gene Expression Microarray Data Identify Hub Genes Involved in Osteoarthritis. Front Genet 2022; 13:870590. [PMID: 35734433 PMCID: PMC9207392 DOI: 10.3389/fgene.2022.870590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/25/2022] [Indexed: 11/28/2022] Open
Abstract
The present study was performed to explore the underlying molecular mechanisms and screen hub genes of osteoarthritis (OA) via bioinformatics analysis. In total, twenty-five OA synovial tissue samples and 25 normal synovial tissue samples were derived from three datasets, namely, GSE55457, GSE55235, and GSE1919, and were used to identify the differentially expressed genes (DEGs) of OA by R language. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). A Venn diagram was built to show the potential hub genes identified in all three datasets. The STRING database was used for constructing the protein–protein interaction (PPI) networks and submodules of DEGs. We identified 507 upregulated and 620 downregulated genes. Upregulated DEGs were significantly involved in immune response, MHC class II receptor activity, and presented in the extracellular region, while downregulated DEGs were mainly enriched in response to organic substances, extracellular region parts, and cadmium ion binding. Results of KEGG analysis indicated that the upregulated DEGs mainly existed in cell adhesion molecules (CAMs), while downregulated DEGs were significantly involved in the MAPK signaling pathway. A total of eighteen intersection genes were identified across the three datasets. These include Nell-1, ATF3, RhoB, STC1, and VEGFA. In addition, 10 hub genes including CXCL12, CXCL8, CCL20, and CCL4 were found in the PPI network and module construction. Identification of DEGs and hub genes associated with OA may be helpful for revealing the molecular mechanisms of OA and further promotes the development of relevant biomarkers and drug targets.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Dazhi Zou
- Department of Spine Surgery, Longhui People’s Hospital, Shaoyang, China
| | - Rongjun Wan
- Branch of National Clinical Research Center for Respiratory Disease, Department of Respiratory Medicine, National Key Clinical Specialty, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Jie Liu
- Department of Cardiology, The Fourth Hospital of Changsha, Changsha, China
| | - Qiong Zhou
- Department of Cardiology, The Fourth Hospital of Changsha, Changsha, China
| | - Zhen Zhou
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Cheng Tao
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Tang Liu, ; Cheng Tao,
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Tang Liu, ; Cheng Tao,
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14
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Shetty A, Tripathi SK, Junttila S, Buchacher T, Biradar R, Bhosale S, Envall T, Laiho A, Moulder R, Rasool O, Galande S, Elo L, Lahesmaa R. A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation. Nucleic Acids Res 2022; 50:4938-4958. [PMID: 35511484 PMCID: PMC9122603 DOI: 10.1093/nar/gkac256] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findings in human. Here, we characterized the human-specific roles of three AP-1 transcription factors, FOSL1, FOSL2 and BATF, during early stages of Th17 differentiation. Our results demonstrate that FOSL1 and FOSL2 co-repress Th17 fate-specification, whereas BATF promotes the Th17 lineage. Strikingly, FOSL1 was found to play different roles in human and mouse. Genome-wide binding analysis indicated that FOSL1, FOSL2 and BATF share occupancy over regulatory regions of genes involved in Th17 lineage commitment. These AP-1 factors also share their protein interacting partners, which suggests mechanisms for their functional interplay. Our study further reveals that the genomic binding sites of FOSL1, FOSL2 and BATF harbour hundreds of autoimmune disease-linked SNPs. We show that many of these SNPs alter the ability of these transcription factors to bind DNA. Our findings thus provide critical insights into AP-1-mediated regulation of human Th17-fate and associated pathologies.
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Affiliation(s)
| | | | | | | | - Rahul Biradar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Department of Biochemistry and Molecular Biology, Protein Research Group, University of Southern Denmark, Campusvej 55, Odense M, DK 5230, Denmark
| | - Tapio Envall
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
- Department of Life Sciences, Shiv Nadar University, Delhi-NCR
| | - Laura L Elo
- Correspondence may also be addressed to Laura Elo. Tel: +358 29 450 2090;
| | - Riitta Lahesmaa
- To whom correspondence should be addressed. Tel: +358 29 450 2415;
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15
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Xu J, Yan Z, Wu G, Zheng Y, Liao X, Zou F. Identification of key genes and pathways associated with sex difference in osteoarthritis based on bioinformatics analysis. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2022; 22:393-400. [PMID: 36046996 PMCID: PMC9438520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES The present study aimed to identify different key genes and pathways between postmenopausal females and males by studying differentially expressed genes (DEGs). METHODS GSE32317 and GSE55457 gene expression data were downloaded from the GEO database, and DEGs were discovered using R software to obtain overlapping DEGs. The interaction between overlapping DEGs was further analyzed by establishing the protein-protein interaction (PPI) network. Finally, GO and KEGG were used for enrichment analysis. RESULTS 924 overlapping DEGs between postmenopausal women and men with osteoarthritis (OA) were identified, including 674 up-regulated genes and 249 down-regulated ones. And 10 hub genes were identified in the PPI network, including BMP4, KDM6A, JMJD1C, NFATC1, PRKX, SRF, ZFX, LAMTOR5, UFD1L and AMBN. The findings of the functional enrichment analysis suggested that these genes were predominantly expressed in MAPK signaling pathway as well as the Thyroid hormone signaling pathway, indicating that those two pathways may be involved in onset and disease progression of OA in postmenopausal patients. CONCLUSION BMP4, KDM6A, JMJD1C, PRKX, ZFX and LAMTOR5 are expected to play crucial roles in disease development in postmenopausal patients and may be ideal targets or prognostic markers for the treatment of OA.
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Affiliation(s)
- Junchang Xu
- Department of Orthopeadics, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China,Corresponding author: Junchang Xu, Department of Orthopeadics, Xiangyang No.1 people’s Hospital, Hubei University of Medicine, No. 15 Jiefang Road, Fancheng District, Xiangyang, 441000, Hubei Province, China E-mail:
| | - Zijian Yan
- Department of Orthopeadics, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Guihua Wu
- Department of General Surgery, Affiliated Hospital of Xiangyang Vocational and Technical College, Xiangyang, China
| | - Yongling Zheng
- Department of Orthopeadics, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Xiaolong Liao
- Department of Orthopeadics, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
| | - Feng Zou
- Department of Orthopeadics, Xiangyang No.1 People’s Hospital, Hubei University of Medicine, Xiangyang, China
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16
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Li J, Huan J, Yang F, Chen H, Wang M, Heng X. Identification and Validation of a Seizure-Free-Related Gene Signature for Predicting Poor Prognosis in Lower-Grade Gliomas. Int J Gen Med 2021; 14:7399-7410. [PMID: 34754221 PMCID: PMC8570923 DOI: 10.2147/ijgm.s329745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
Background Lower-grade gliomas (LGGs) patients presented seizure-free have a worse survival than those presented with seizures. However, the current knowledge on its potential value in LGGs remains scarce. Purpose This study aimed to identify a novel gene signature associated with seizures-free for predicting poor prognosis for LGGs patients. Materials and Methods The RNA expression and clinical information of LGGs patients were downloaded from the Cancer Genome Atlas database. Differentially expressed genes (DEGs) were screened out between LGGs patients presented seizures-free and seizures. The novel gene signature was constructed by Lasso and multivariate regression analyses for predicting prognosis in LGGs. Its prognostic value was assessed and validated by Kaplan-Meier analyses and receiver operating characteristic (ROC) curves. Multivariate regression analysis was applied to identify the independent prognostic value of the gene signature. Furthermore, bioinformatics analysis was performed to elucidate the molecular mechanisms. Results A total of 253 DEGs were screened out between LGG patients presented with seizures and free of seizures. A 5-gene signature (HIST1H4F, HORMAD2, LILRA3, PRSS33, and TBX20 genes) was constructed from these 253 DEGs. Kaplan-Meier analyses and ROC curves assessed and validated the good performance of the 5-gene signature in differentiating and predicting prognosis of high- and low-risk patients. Multivariate regression analysis determined the independent prognostic value of the 5-gene signature. According to bioinformatics analysis, DEGs were mainly enriched in biological processes related to positive regulation of transcription from RNA polymerase II promoter, G-protein coupled receptor signaling pathway, and pathways of cytokine-cytokine receptor interaction, chemokine signaling pathway. Conclusion Our findings suggested that the 5-gene signature might serve as a potential prognostic biomarker and provide guidance for the personalized LGGs management.
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Affiliation(s)
- Jinxing Li
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, 276000, Shandong, People's Republic of China
| | - Jing Huan
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China
| | - Fu Yang
- Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, People's Republic of China.,Department of Neurosurgery, Linyi People's Hospital, Linyi, 276000, Shandong, People's Republic of China
| | - Haixin Chen
- Department of Neurosurgery, Linyi People's Hospital, Linyi, 276000, Shandong, People's Republic of China.,Weifang Medical University, Weifang, 261053, Shandong, People's Republic of China
| | - Mingguang Wang
- Department of Neurosurgery, Linyi People's Hospital, Linyi, 276000, Shandong, People's Republic of China
| | - Xueyuan Heng
- Department of Neurosurgery, Linyi People's Hospital, Linyi, 276000, Shandong, People's Republic of China
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17
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Weng PW, Yadav VK, Pikatan NW, Fong IH, Lin IH, Yeh CT, Lee WH. Novel NFκB Inhibitor SC75741 Mitigates Chondrocyte Degradation and Prevents Activated Fibroblast Transformation by Modulating miR-21/GDF-5/SOX5 Signaling. Int J Mol Sci 2021; 22:11082. [PMID: 34681754 PMCID: PMC8538686 DOI: 10.3390/ijms222011082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/04/2021] [Accepted: 10/09/2021] [Indexed: 02/07/2023] Open
Abstract
Osteoarthritis (OA) is a common articular disease manifested by the destruction of cartilage and compromised chondrogenesis in the aging population, with chronic inflammation of synovium, which drives OA progression. Importantly, the activated synovial fibroblast (AF) within the synovium facilitates OA through modulating key molecules, including regulatory microRNAs (miR's). To understand OA associated pathways, in vitro co-culture system, and in vivo papain-induced OA model were applied for this study. The expression of key inflammatory markers both in tissue and blood plasma were examined by qRT-PCR, western blot, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA) and immunofluorescence assays. Herein, our result demonstrated, AF-activated human chondrocytes (AC) exhibit elevated NFκB, TNF-α, IL-6, and miR-21 expression as compared to healthy chondrocytes (HC). Importantly, AC induced the apoptosis of HC and inhibited the expression of chondrogenesis inducers, SOX5, TGF-β1, and GDF-5. NFκB is a key inflammatory transcription factor elevated in OA. Therefore, SC75741 (an NFκB inhibitor) therapeutic effect was explored. SC75741 inhibits inflammatory profile, protects AC-educated HC from apoptosis, and inhibits miR-21 expression, which results in the induced expression of GDF-5, SOX5, TGF-β1, BMPR2, and COL4A1. Moreover, ectopic miR-21 expression in fibroblast-like activated chondrocytes promoted osteoblast-mediated differentiation of osteoclasts in RW264.7 cells. Interestingly, in vivo study demonstrated SC75741 protective role, in controlling the destruction of the articular joint, through NFκB, TNF-α, IL-6, and miR-21 inhibition, and inducing GDF-5, SOX5, TGF-β1, BMPR2, and COL4A1 expression. Our study demonstrated the role of NFκB/miR-21 axis in OA progression, and SC75741's therapeutic potential as a small-molecule inhibitor of miR-21/NFκB-driven OA progression.
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Affiliation(s)
- Pei-Wei Weng
- Department of Orthopaedics, School of Medicine, College of Medicine, Taipei Medical University, Taipei City 110, Taiwan;
- Department of Orthopaedics, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei City 110, Taiwan
| | - Vijesh Kumar Yadav
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (V.K.Y.); (N.W.P.); (I.-H.F.); (C.-T.Y.)
| | - Narpati Wesa Pikatan
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (V.K.Y.); (N.W.P.); (I.-H.F.); (C.-T.Y.)
| | - Iat-Hang Fong
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (V.K.Y.); (N.W.P.); (I.-H.F.); (C.-T.Y.)
| | - I-Hsin Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei City 110, Taiwan
- Division of Periodontics, Department of Dentistry, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan
| | - Chi-Tai Yeh
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (V.K.Y.); (N.W.P.); (I.-H.F.); (C.-T.Y.)
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu City 30015, Taiwan
| | - Wei-Hwa Lee
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (V.K.Y.); (N.W.P.); (I.-H.F.); (C.-T.Y.)
- Department of Pathology, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan
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18
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Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS OMEGA 2021; 6:24834-24847. [PMID: 34604665 PMCID: PMC8482465 DOI: 10.1021/acsomega.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among the latter, FOSL1 and FOSL2 modulate the effector functions of Th17 cells. However, the molecular mechanisms underlying these effects are unclear, owing to the poorly characterized protein interaction networks of FOSL factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a significant fraction of these interactors to be associated with RNA-binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17 fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL proteins that potentially govern Th17 cell differentiation and associated pathologies.
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Affiliation(s)
- Ankitha Shetty
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Santosh D. Bhosale
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- Protein
Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Subhash Kumar Tripathi
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
| | - Tanja Buchacher
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Rahul Biradar
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Riitta Lahesmaa
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
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19
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Nikopensius T, Niibo P, Haller T, Jagomägi T, Voog-Oras Ü, Tõnisson N, Metspalu A, Saag M, Pruunsild C. Association analysis of juvenile idiopathic arthritis genetic susceptibility factors in Estonian patients. Clin Rheumatol 2021; 40:4157-4165. [PMID: 34101054 PMCID: PMC8463396 DOI: 10.1007/s10067-021-05756-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Background Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic condition of childhood. Genetic association studies have revealed several JIA susceptibility loci with the strongest effect size observed in the human leukocyte antigen (HLA) region. Genome-wide association studies have augmented the number of JIA-associated loci, particularly for non-HLA genes. The aim of this study was to identify new associations at non-HLA loci predisposing to the risk of JIA development in Estonian patients. Methods We performed genome-wide association analyses in an entire JIA case–control sample (All-JIA) and in a case–control sample for oligoarticular JIA, the most prevalent JIA subtype. The entire cohort was genotyped using the Illumina HumanOmniExpress BeadChip arrays. After imputation, 16,583,468 variants were analyzed in 263 cases and 6956 controls. Results We demonstrated nominal evidence of association for 12 novel non-HLA loci not previously implicated in JIA predisposition. We replicated known JIA associations in CLEC16A and VCTN1 regions in the oligoarticular JIA sample. The strongest associations in the All-JIA analysis were identified at PRKG1 (P = 2,54 × 10−6), LTBP1 (P = 9,45 × 10−6), and ELMO1 (P = 1,05 × 10−5). In the oligoarticular JIA analysis, the strongest associations were identified at NFIA (P = 5,05 × 10−6), LTBP1 (P = 9,95 × 10−6), MX1 (P = 1,65 × 10−5), and CD200R1 (P = 2,59 × 10−5). Conclusion This study increases the number of known JIA risk loci and provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. The reported loci are involved in molecular pathways of immunological relevance and likely represent genomic regions that confer susceptibility to JIA in Estonian patients.
Key Points • Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease with heterogeneous presentation and genetic predisposition. • Present genome-wide association study for Estonian JIA patients is first of its kind in Northern and Northeastern Europe. • The results of the present study increase the knowledge about JIA risk loci replicating some previously described associations, so adding weight to their relevance and describing novel loci. • The study provides additional evidence for the existence of overlapping genetic risk loci between JIA and other autoimmune diseases, particularly rheumatoid arthritis. |
Supplementary Information The online version contains supplementary material available at 10.1007/s10067-021-05756-x.
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Affiliation(s)
- Tiit Nikopensius
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.
| | - Priit Niibo
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Toomas Haller
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Triin Jagomägi
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Ülle Voog-Oras
- Institute of Dentistry, University of Tartu, Tartu, Estonia.,Stomatology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Neeme Tõnisson
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Mare Saag
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Chris Pruunsild
- Children's Clinic, Tartu University Hospital, Tartu, Estonia.,Children's Clinic, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
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20
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Maglaviceanu A, Wu B, Kapoor M. Fibroblast-like synoviocytes: Role in synovial fibrosis associated with osteoarthritis. Wound Repair Regen 2021; 29:642-649. [PMID: 34021514 DOI: 10.1111/wrr.12939] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/02/2021] [Accepted: 05/08/2021] [Indexed: 12/12/2022]
Abstract
The synovial membrane undergoes a variety of structural changes throughout the pathogenesis of osteoarthritis (OA), including the development of fibrosis. Fibroblast-like synoviocytes (FLS) are a heterogenous cell population of the synovium that are suggested to drive the fibrotic response, but the exact mechanisms associated with their activation in OA remain unclear. Once activated, FLS are suggested to acquire a myofibroblast-like phenotype that drives fibrogenesis through excessive extracellular matrix (ECM) component deposition and an enhanced contractile function. In this review, we define FLS in the synovium, discuss how select extracellular or endogenous factors potentially induce their activation in OA, and describe how the activity of myofibroblast-like cells affects the structure of the synovial membrane.
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Affiliation(s)
- Anca Maglaviceanu
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Brian Wu
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Surgery, University of Toronto, Toronto, Ontario, Canada
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21
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Yao B, Zhou Z, Zhang M, Leng X, Zhao D. Investigating the molecular control of deer antler extract on articular cartilage. J Orthop Surg Res 2021; 16:8. [PMID: 33407721 PMCID: PMC7788833 DOI: 10.1186/s13018-020-02148-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Deer antler is considered as a precious traditional Chinese medicinal material and has been widely used to reinforce kidney's yang, nourish essence, and strengthen bone function. The most prominent bioactive components in deer antler are water-soluble proteins that play potential roles in bone formation and repair. The aim of this study was to explore the molecular control and therapeutic targets of deer antler extract (DAE) on articular cartilage. METHODS DAE was prepared as previously described. All rats were randomly divided into Blank group and DAE group (10 rats per group) after 7-day adaptive feeding. The rats in DAE group were orally administrated with DAE at a dose of 0.2 g/kg per day for 3 weeks, and the rats in Blank group were fed with drinking water. Total RNA was isolated from the articular cartilage of knee joints. RNA sequencing (RNA-seq) experiment combined with quantitative real-time polymerase chain reaction (qRT-PCR) verification assay was carried out to explore the molecular control and therapeutic targets of DAE on articular cartilage. RESULTS We demonstrated that DAE significantly increased the expression levels of functional genes involved in cartilage formation, growth, and repair and decreased the expression levels of susceptibility genes involved in the pathophysiology of osteoarthritis. CONCLUSIONS DAE might serve as a candidate supplement for maintaining cartilage homeostasis and preventing cartilage degeneration and inflammation. These effects were possibly achieved by accelerating the expression of functional genes involved in chondrocyte commitment, survival, proliferation, and differentiation and suppressing the expression of susceptibility genes involved in the pathophysiology of osteoarthritis. Thus, our findings will contribute towards deepening the knowledge about the molecular control and therapeutic targets of DAE on the treatment of cartilage-related diseases.
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Affiliation(s)
- Baojin Yao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Zhenwei Zhou
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Mei Zhang
- Innovation Practice Center, Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Xiangyang Leng
- The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 130117 China
| | - Daqing Zhao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117 China
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22
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Zhang Y, Yang Y, Wang C, Wan S, Yao Z, Zhang Y, Liu J, Zhang C. Identification of Diagnostic Biomarkers of Osteoarthritis Based on Multi-Chip Integrated Analysis and Machine Learning. DNA Cell Biol 2020; 39:2245-2256. [PMID: 33064574 DOI: 10.1089/dna.2020.5552] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The pathogenesis of osteoarthritis (OA) is still unclear. It is therefore important to identify relevant diagnostic marker genes for OA. We performed an integrated analysis with multiple microarray data cohorts to identify potential transcriptome markers of OA development. Further, to identify OA diagnostic markers, we established gene regulatory networks based on the protein-protein interaction network involved in these differentially expressed genes (DEGs). Using support vector machine (SVM) pattern recognition, a diagnostic model for OA prediction and prevention was established. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that 190 DEGs were mainly enriched in pathways like the tumor necrosis factor signaling pathway, interleukin-17 signaling pathway, mitogen-activated protein kinase signaling pathway, nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway, and osteoclast differentiation. Eight hub genes (POSTN, MMP2, CTSG, ELANE, COL3A1, MPO, COL1A1, and COL1A2) were considered potential diagnostic biomarkers for OA, the area under curve (AUC) was >0.95, which showed high accuracy. The sensitivity and specificity of the SVM model of OA based on these eight genes reached 100% in multiple external verification cohorts. Our research provides a theoretical basis for OA diagnosis for clinicians.
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Affiliation(s)
- Yueqi Zhang
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi Yang
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chenzhong Wang
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shengcheng Wan
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhenjun Yao
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinyu Liu
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chi Zhang
- Department of Orthopedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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23
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Genetic landscape and autoimmunity of monocytes in developing Vogt-Koyanagi-Harada disease. Proc Natl Acad Sci U S A 2020; 117:25712-25721. [PMID: 32989127 DOI: 10.1073/pnas.2002476117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a systemic autoimmune disorder affecting multiple organs, including eyes, skin, and central nervous system. It is known that monocytes significantly contribute to the development of autoimmune disease. However, the subset heterogeneity with unique functions and signatures in human circulating monocytes and the identity of disease-specific monocytic populations remain largely unknown. Here, we employed an advanced single-cell RNA sequencing technology to systematically analyze 11,259 human circulating monocytes and genetically defined their subpopulations. We constructed a precise atlas of human blood monocytes, identified six subpopulations-including S100A12, HLA, CD16, proinflammatory, megakaryocyte-like, and NK-like monocyte subsets-and uncovered two previously unidentified subsets: HLA and megakaryocyte-like monocyte subsets. Relative to healthy individuals, cellular composition, gene expression signatures, and activation states were markedly alternated in VKH patients utilizing cell type-specific programs, especially the CD16 and proinflammatory monocyte subpopulations. Notably, we discovered a disease-relevant subgroup, proinflammatory monocytes, which showed a discriminative gene expression signature indicative of inflammation, antiviral activity, and pathologic activation, and converted into a pathologic activation state implicating the active inflammation during VKH disease. Additionally, we found the cell type-specific transcriptional signature of proinflammatory monocytes, ISG15, whose production might reflect the treatment response. Taken together, in this study, we present discoveries on accurate classification, molecular markers, and signaling pathways for VKH disease-associated monocytes. Therapeutically targeting this proinflammatory monocyte subpopulation would provide an attractive approach for treating VKH, as well as other autoimmune diseases.
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24
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Yang Y, You X, Cohen JD, Zhou H, He W, Li Z, Xiong Y, Yu T. Sex Differences in Osteoarthritis Pathogenesis: A Comprehensive Study Based on Bioinformatics. Med Sci Monit 2020; 26:e923331. [PMID: 32255771 PMCID: PMC7163332 DOI: 10.12659/msm.923331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Osteoarthritis (OA) is a common disorder in the elderly. OA influences the daily life of patients and has become a worldwide health problem. It is still unclear whether the pathogenesis mechanism is different between males and females. This study investigated the differentially expressed genes (DEGs) and explored the different signaling pathways of OA between males and females. Material/Methods Data sets of GSE55457, GSE55584, and GSE12021 were retrieved from Gene Expression Omnibus to conduct DEGs analysis. Enrichment analysis of Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology term was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatics tool. The protein interaction network was constructed in Cytoscape 3.7.2. qRT-PCR was then performed to validate the expression of hub genes in OA patients and healthy people. Results In total, 4 co-upregulated and 10 co-downregulated genes were identified. We found that enriched pathways were different between males and females. BCL2L1, EEF1A1, EEF2, HNRNPD, and PABPN1 were considered as hub genes in OA pathogenesis in males, while EEF2, EEF1A1, RPL37A, FN1 were considered as hub genes in OA pathogenesis in females. Consistent with the bioinformatics analysis, the qRT-PCR analysis also showed that the gene expression of BCL2L1, HNRNPD, and PABPN1 was significantly lower in male OA patients. In contrast, EEF2, EEF1A1, and RPL37A were significantly lower in female OA patients. Conclusions The DEGs identified may be involved in different OA disease progression mechanisms between males and females, and they are considered as treatment targets or prognosis markers for males and females. The pathogenesis mechanism is sex-dependent.
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Affiliation(s)
- Yunfeng Yang
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
| | - Xiaomeng You
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jordan Daniel Cohen
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Haichao Zhou
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
| | - Wenbao He
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
| | - Zihua Li
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
| | - Yuan Xiong
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (mainland)
| | - Tao Yu
- Department of Orthopedic Surgery, Tongji Hospital, Tongji University School of Medicine, Shanghai, China (mainland)
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25
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Lü G, Li L, Wang B, Kuang L. LINC00623/miR-101/HRAS axis modulates IL-1β-mediated ECM degradation, apoptosis and senescence of osteoarthritis chondrocytes. Aging (Albany NY) 2020; 12:3218-3237. [PMID: 32062610 PMCID: PMC7066905 DOI: 10.18632/aging.102801] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/19/2020] [Indexed: 05/12/2023]
Abstract
Chondrocyte apoptosis and extracellular matrix (ECM) degeneration have been implicated in the pathogenesis of osteoarthritis (OA). Based on previously reported microarray analysis, HRAS (Harvey rat sarcoma viral oncogene homolog), a member of the RAS protein family, was chosen as a potential regulator of OA chondrocyte apoptosis and ECM degradation. HRAS expression was downregulated in OA tissues, particularly in mild-OA tissues. HRAS overexpression partially attenuated IL-1β-induced OA chondrocyte apoptosis and ECM degradation. Similar to HRAS, the long non-coding RNA LINC00623 was downregulated in OA tissues. LINC00623 knockdown enhanced IL-1β-induced OA chondrocyte apoptosis and ECM degradation, which could be partially reversed by HRAS overexpression. It has been reported that lncRNAs act as ceRNAs of miRNAs to exert their function. Herein, miR-101 was predicted to bind to both LINC00623 and HRAS, which was further confirmed by luciferase reporter and RIP assays. LINC00623 competed with HRAS for miR-101 binding, therefore reducing the inhibitory effect of miR-101 on HRAS expression. More importantly, the effect of LINC00623 was partially eliminated by miR-101 inhibition. Overall, the LINC00623/miR-101/HRAS axis modulates OA chondrocyte apoptosis, senescence and ECM degradation through MAPK signaling, which might play a critical role in OA development.
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Affiliation(s)
- Guohua Lü
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Lei Li
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Bing Wang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Lei Kuang
- Department of Spine Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
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26
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Zhou W, Wu J, Zhu Y, Meng Z, Liu X, Liu S, Ni M, Jia S, Zhang J, Guo S. Study on the mechanisms of compound Kushen injection for the treatment of gastric cancer based on network pharmacology. BMC Complement Med Ther 2020; 20:6. [PMID: 32020871 PMCID: PMC7076865 DOI: 10.1186/s12906-019-2787-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/04/2019] [Indexed: 12/24/2022] Open
Abstract
Background As an effective prescription for gastric cancer (GC), Compound Kushen Injection (CKI) has been widely used even though few molecular mechanism analyses have been carried out. Methods In this study, we identified 16 active ingredients and 60 GC target proteins. Then, we established a compound-predicted target network and a GC target protein-protein interaction (PPI) network by Cytoscape 3.5.1 and systematically analyzed the potential targets of CKI for the treatment of GC. Finally, molecular docking was applied to verify the key targets. In addition, we analyzed the mechanism of action of the predicted targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses. Results The results showed that the potential targets, including CCND1, PIK3CA, AKT1, MAPK1, ERBB2, and MMP2, are the therapeutic targets of CKI for the treatment of GC. Functional enrichment analysis indicated that CKI has a therapeutic effect on GC by synergistically regulating some biological pathways, such as the cell cycle, pathways in cancer, the PI3K-AKT signaling pathway, the mTOR signaling pathway, and the FoxO signaling pathway. Moreover, molecular docking simulation indicated that the compounds had good binding activity to PIK3CA, AKT1, MAPK1, ERBB2, and MMP2 in vivo. Conclusion This research partially highlighted the molecular mechanism of CKI for the treatment of GC, which has great potential in the identification of the effective compounds in CKI and biomarkers to treat GC.
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Affiliation(s)
- Wei Zhou
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China.
| | - Yingli Zhu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Shuyu Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Mengwei Ni
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Shanshan Jia
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Jingyuan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
| | - Siyu Guo
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 11 of North Three-ring East Road, Chao Yang District, Beijing, China
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Zhang G, Gu M, Xu Y, Wu Z. A comprehensive analysis on the effects of 1,25(OH)2D3 on primary chondrocytes cultured from patients with osteoarthritis. Gene 2019; 730:144322. [PMID: 31899303 DOI: 10.1016/j.gene.2019.144322] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022]
Abstract
AIM This study aimed to investigate the effect of 1,25-dihydroxy-vitamin D3 (1,25(OH)2D3) on primary chondrocytes cultured from patients with osteoarthritis (OA). METHOD Primary chondrocytes isolated from the tibial plateau of female OA patients were characterized by immunocytochemistry analysis. Using Cell Counting Kit-8 (CCK-8), cell viability was measured to select suitable 1,25(OH)2D3 concentrations for treating chondrocytes. RNA-sequencing was performed on primary chondrocytes treated with or without 1,25(OH)2D3. Differentially expressed genes (DEGs) as well as gene ontology (GO)-biological process (BP) and pathways affected by 1,25(OH)2D3 were identified. Protein-protein interaction (PPI) network was constructed, and the hub nodes in the PPI network were identified. qRT-PCR was conducted to confirm the expression levels of six DEGs. RESULTS Positive collagen II staining confirmed the successful isolation of primary chondrocytes. CCK-8 assay showed maximal primary chondrocyte survival rate when treated with 10-5 μmol/L of 1,25(OH)2D3 for 72 h. RNA-sequencing results identified a total of 1036 DEGs, including 593 upregulated and 443 downregulated genes from 1,25(OH)2D3 treated and untreated cells. Further functional enrichment analyses showed the association of these DEGs with GO-BP terms such as response to the stimulus, cell proliferation, angiogenesis, and regulation of cell motility, and KEGG pathways, including TNF signaling pathway, IL-17 signaling pathway, cytokine-cytokine receptor interaction, and NF-kappa B signaling pathway. PPI network identified UBC, FOS, IFIT1, CDK1, and ISG15 as the hub nodes in the network. qRT-PCR results were in alignment with the results of RNA-sequencing. CONCLUSION Our study might provide a theoretical basis for the use of vitamin D in treating OA.
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Affiliation(s)
- Guoning Zhang
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China.
| | - Mengzhen Gu
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China.
| | - Yingjia Xu
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China.
| | - Zongming Wu
- Department of Orthopedics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China.
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28
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Identification of Key Genes and Pathways Associated with Sex Differences in Osteoarthritis Based on Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3482751. [PMID: 31886203 PMCID: PMC6925789 DOI: 10.1155/2019/3482751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Sex differences have been suggested to play critical roles in the pathophysiology of osteoarthritis (OA), resulting in sex-specific prevalence and incidence. However, their roles in the development of OA remain largely unknown. The aim of this study was to screen out key genes and pathways mediating biological differences between OA females after menopause and OA males. First, the gene expression data of GSE36700 and GSE55457 were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between sexes were identified using R software, respectively. The overlapping DEGs were obtained. Then, protein-protein interactive (PPI) network was constructed to further analyze interactions between the overlapping DEGs. Finally, enrichment analyses were separately performed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes tools. In our results, a total of 278 overlapping DEGs were identified between OA females after menopause and OA males, including 219 upregulated and 59 downregulated genes. In the PPI network, seven hub genes were identified, including EGF, ERBB2, CDC42, PIK3R2, LCK, CBL, and STAT1. Functional enrichment analysis revealed that these genes were mainly enriched in PI3K-Akt signaling pathway, osteoclast differentiation, and focal adhesion. In conclusion, the results in the current study suggest that pathways of PI3K-Akt, osteoclast differentiation, and focal adhesion may play important roles in the development of OA females after menopause. EGFR, ERBB2, CDC42, and STAT1 may be key genes related to OA progression in postmenopausal women and may be promising therapeutic targets for OA.
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29
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Zhou J, Li C, Yu A, Jie S, Du X, Liu T, Wang W, Luo Y. Bioinformatics analysis of differentially expressed genes involved in human developmental chondrogenesis. Medicine (Baltimore) 2019; 98:e16240. [PMID: 31277141 PMCID: PMC6635276 DOI: 10.1097/md.0000000000016240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Osteoarthritis (OA), also known as degenerative arthritis, affects millions of people all over the world. OA occurs when the cartilage wears down over time, which is a worldwide complaint. The aim of this study was to screen and verify hub genes involved in developmental chondrogenesis as well as to explore potential molecular mechanisms.The expression profiles of GSE51812 were downloaded from the Gene Expression Omnibus (GEO) database, which contained 9 samples, including 6-week pre-chondrocytes (PC, 6 independent specimens) and 17-week fetal periarticular resting chondrocytes (RC, 3 independent specimens). The raw data were integrated to obtain differentially expressed genes (DEGs) and were further analyzed with bioinformatics analysis. The Gene Ontology (GO) and pathway enrichment of DEGs were conducted via Database for Annotation, Visualization, and Integrated Discovery (DAVID). The protein-protein interaction (PPI) networks of the DEGs were constructed based on data from the search tool for the retrieval of interacting genes (STRING) database. An intersection figure was provided to show the relationship between the DEGs identified in this study and genes from any existed related studies.A total of 9486 DEGs, including 4821 upregulated genes and 4665 downregulated genes were observed. The top 30 developmental chondrogenesis associated genes were identified, including matrix metalloproteinase (MMP)1, MMP3, MMP13, prostaglandin-endoperoxide synthase 2 (PTGS2), and so on. The majority of DEGs, including PTGS2, CCL20, CHI3L1, LIF, CXCL8, and CXCL12 were intensively enriched in immune-associated biological process terms, including inflammatory, and immune responses. Additionally, the majority of DEGs were mainly enriched in NF-kappa β (NF-kβ) signaling pathway and tumor necrosis factor (TNF) signaling pathway. The hub genes identified in STRING and Cytoscape databases included MMP1, MMP3, MMP13, PTGS2 and so on. Among the top 30 upregulated and downregulated DEGs, there were 15 genes have been reported to be associated with OA or developmental chondrogenesis.This large scale gene expression study observed genes associated with human developmental chondrogenesis and their relative GO function, which may offer opportunities for the research for cartilage tissue engineering and novel insights into the prevention of OA in the near future.
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Affiliation(s)
- Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital
- Department of Sports Medicine Research Center, Central South University, Changsha, Hunan
| | - Chenxi Li
- Department of Clinical Medicine, School of Medicine
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong
| | - Anqi Yu
- Department of Anesthesiology, The Second Xiangya Hospital
| | - Shuo Jie
- Department of Orthopedics, The Second Xiangya Hospital
| | - Xiadong Du
- Department of Orthopedics, The Second Xiangya Hospital
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital
- State Key Laboratory of Powder Metallurgy, Central South University
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital
| | - Yingquan Luo
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Li HZ, Lu HD. Transcriptome analyses identify key genes and potential mechanisms in a rat model of osteoarthritis. J Orthop Surg Res 2018; 13:319. [PMID: 30551734 PMCID: PMC6295024 DOI: 10.1186/s13018-018-1019-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 11/26/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Osteoarthritis (OA) is one of the most common degenerative diseases of the joints worldwide, but still the pathogenesis of OA is largely unknown. The purpose of our study is to clarify key candidate genes and relevant signaling pathways in a surgical-induced OA rat model. METHODS The microarray raw data of GSE8077 was downloaded from GEO datasets. GeoDiver were employed to screen differentially-expressed genes (DEGs). Enrichment analyses of DEGs were performed using Metascape. Construction of protein-protein interaction (PPI) network and identification of key genes were conducted using STRING, Cytoscape v3.6.0, and Centiscape2.2. Furthermore, miRDB and Cytoscape v3.6.0 were used for visualization of miRNA-mRNA regulatory network. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for predicted miRNAs was undertaken using DIANA-miRPath v3.0. RESULTS Several DEGs (188 in comparison between OA and sham-operated group and 160 in comparison between OA and contralateral group) were identified. DEGs mainly enriched in vasculature development, regulation of cell migration, response to growth factor (Gene ontology), and ECM-receptor interaction (KEGG). Two comparison cohorts shared 79 intersection genes, and of these, Ccl2, Col4a1, Col1a1, Aldh1a3, and Itga8 were defined as the hub genes. Predicted miRNAs of seven DEGs from sub-networks mainly enriched in MAPK signaling pathway. CONCLUSION The current study shows that some key genes and pathways, such as Ccl2, Col4a1, Col1a1, Aldh1a3, Itga8, ECM-receptor interaction, and MAPK signaling pathway may be associated with OA progression and act as potential biomarkers and therapeutic targets for OA.
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Affiliation(s)
- Hui-Zi Li
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.,Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong Province, China
| | - Hua-Ding Lu
- Department of Orthopaedics, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China. .,Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong Province, China.
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Xiang S, Li Z, Bian Y, Weng X. Identification of changed expression of mRNAs and lncRNAs in osteoarthritic synovium by RNA-sequencing. Gene 2018; 685:55-61. [PMID: 30393192 DOI: 10.1016/j.gene.2018.10.076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/25/2018] [Accepted: 10/26/2018] [Indexed: 01/15/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently reported to regulate the homeostasis of cartilage in osteoarthritis (OA), but their regulatory roles in OA synovium remain elusive. This study aimed to identify the differentially expressed mRNAs and lncRNAs in OA synovium and further explore the function of differentially expressed lncRNAs in OA progression through bioinformatics analysis. We started with RNA-sequencing in 5 OA synovium samples and 5 healthy controls to compare the expression of mRNAs and lncRNAs. GO analysis and KEGG pathway analysis were performed to annotate the function of differentially expressed mRNAs. Then real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was admitted in 17 osteoarthritic synovium and 18 healthy controls to confirm the changes of the expression of the selected lncRNAs. LncRNA-mRNA co-expression network was constructed to predict the potential molecular regulatory mechanisms of specifically expressed lncRNAs in OA synovium. 384 mRNAs and 17 lncRNAs were detected to be differentially expressed in OA synovium. The expressions of 4 lncRNAs were confirmed by qRT-PCR. We found the differentially expression lncRNAs could potentially regulate OA progression through pathways regarding to immune response through the lncRNA-mRNA network and further annotation for co-expression mRNAs. Our results indicated that lncRNAs may play key roles in OA synovitis and may have potential value in OA diagnosis.
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Affiliation(s)
- Shuai Xiang
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing 100730, China
| | - Zeng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing 100730, China
| | - Yanyan Bian
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing 100730, China
| | - Xisheng Weng
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing 100730, China.
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Zhu H, Wu LF, Mo XB, Lu X, Tang H, Zhu XW, Xia W, Guo YF, Wang MJ, Zeng KQ, Wu J, Qiu YH, Lin X, Zhang YH, Liu YZ, Yi NJ, Deng FY, Lei SF. Rheumatoid arthritis–associated DNA methylation sites in peripheral blood mononuclear cells. Ann Rheum Dis 2018; 78:36-42. [DOI: 10.1136/annrheumdis-2018-213970] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
ObjectivesTo identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism.MethodsWe performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells.ResultsA total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation–mRNA–RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2).ConclusionsThis multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.
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Li L, Lv G, Wang B, Kuang L. The role of lncRNA XIST/miR-211 axis in modulating the proliferation and apoptosis of osteoarthritis chondrocytes through CXCR4 and MAPK signaling. Biochem Biophys Res Commun 2018; 503:2555-2562. [PMID: 30005876 DOI: 10.1016/j.bbrc.2018.07.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/20/2022]
Abstract
Long noncoding RNAs (lncRNAs) participate in multiple diverse diseases, including osteoarthritis (OA). Here, we explored the role of lncRNA XIST in OA and identified the potential molecular mechanisms. The expression of XIST in cartilage samples in patients with OA was significantly upregulated. XIST knockdown remarkably suppressed IL-1β-suppressed OA chondrocyte proliferation while promoted IL-1β-induced cell apoptosis. By employing online tools, miRNAs related to CXCR4, a major contributor to chondrocyte apoptosis, and XIST were selected. miR-211 expression could be significantly inhibited by IL-1β stimulation, and miR-211 negatively regulated XIST expression and CXCR4 protein levels. Through direct binding, XIST served as a ceRNA for miR-211 to counteract miR-211-mediated CXCR4 repression, thereby modulating chondrocyte proliferation and apoptosis through downstream MAPK signaling. In OA tissues, miR-211 expression was significantly downregulated while CXCR4 mRNA expression was upregulated. miR-211 was negatively correlated with XIST and CXCR4, respectively, while XIST and CXCR4 was positively correlated in tissue samples. In conclusion, the study revealed that lncRNA XIST can promote the proliferation of OA chondrocytes and promote apoptosis through the miR-211/CXCR4 axis. Thus, lncRNA XIST might be considered as a potential therapeutic target for OA treatment.
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Affiliation(s)
- Lei Li
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Guohua Lv
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Bing Wang
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Lei Kuang
- Department of Spine Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
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Guo SM, Wang JX, Li J, Xu FY, Wei Q, Wang HM, Huang HQ, Zheng SL, Xie YJ, Zhang C. Identification of gene expression profiles and key genes in subchondral bone of osteoarthritis using weighted gene coexpression network analysis. J Cell Biochem 2018; 119:7687-7695. [PMID: 29904957 DOI: 10.1002/jcb.27118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 05/04/2018] [Indexed: 02/05/2023]
Abstract
Osteoarthritis (OA) significantly influences the quality life of people around the world. It is urgent to find an effective way to understand the genetic etiology of OA. We used weighted gene coexpression network analysis (WGCNA) to explore the key genes involved in the subchondral bone pathological process of OA. Fifty gene expression profiles of GSE51588 were downloaded from the Gene Expression Omnibus database. The OA-associated genes and gene ontologies were acquired from JuniorDoc. Weighted gene coexpression network analysis was used to find disease-related networks based on 21756 gene expression correlation coefficients, hub-genes with the highest connectivity in each module were selected, and the correlation between module eigengene and clinical traits was calculated. The genes in the traits-related gene coexpression modules were subject to functional annotation and pathway enrichment analysis using ClusterProfiler. A total of 73 gene modules were identified, of which, 12 modules were found with high connectivity with clinical traits. Five modules were found with enriched OA-associated genes. Moreover, 310 OA-associated genes were found, and 34 of them were among hub-genes in each module. Consequently, enrichment results indicated some key metabolic pathways, such as extracellular matrix (ECM)-receptor interaction (hsa04512), focal adhesion (hsa04510), the phosphatidylinositol 3'-kinase (PI3K)-Akt signaling pathway (PI3K-AKT) (hsa04151), transforming growth factor beta pathway, and Wnt pathway. We intended to identify some core genes, collagen (COL)6A3, COL6A1, ITGA11, BAMBI, and HCK, which could influence downstream signaling pathways once they were activated. In this study, we identified important genes within key coexpression modules, which associate with a pathological process of subchondral bone in OA. Functional analysis results could provide important information to understand the mechanism of OA.
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Affiliation(s)
- Sheng-Min Guo
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian-Xiong Wang
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jin Li
- Hepatological Surgery Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Fang-Yuan Xu
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Quan Wei
- Rehabilitation Medicine Department, West China Hospital, Sichuan University, Chengdu, China
| | - Hai-Ming Wang
- Rehabilitation Medicine Department, West China Hospital, Sichuan University, Chengdu, China
| | - Hou-Qiang Huang
- Nursing Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Si-Lin Zheng
- Nursing Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yu-Jie Xie
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Chi Zhang
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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Silva-Vignato B, Coutinho LL, Cesar ASM, Poleti MD, Regitano LCA, Balieiro JCC. Comparative muscle transcriptome associated with carcass traits of Nellore cattle. BMC Genomics 2017; 18:506. [PMID: 28673252 PMCID: PMC5496360 DOI: 10.1186/s12864-017-3897-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 01/16/2023] Open
Abstract
Background Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. Results By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. Conclusion In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3897-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bárbara Silva-Vignato
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil.
| | - Luiz L Coutinho
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Aline S M Cesar
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Mirele D Poleti
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Júlio C C Balieiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
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Brooks J, Watson A, Korcsmaros T. Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:101-109. [PMID: 28373027 PMCID: PMC5414711 DOI: 10.1016/j.gpb.2016.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 12/12/2022]
Abstract
Inflammatory diseases such as inflammatory bowel disease (IBD) require recurrent invasive tests, including blood tests, radiology, and endoscopic evaluation both to diagnose and assess disease activity, and to determine optimal therapeutic strategies. Simple ‘bedside’ biomarkers could be used in all phases of patient management to avoid unnecessary investigation and guide further management. The focal adhesion complex (FAC) has been implicated in the pathogenesis of multiple inflammatory diseases, including IBD, rheumatoid arthritis, and multiple sclerosis. Utilizing omics technologies has proven to be an efficient approach to identify biomarkers from within the FAC in the field of cancer medicine. Predictive biomarkers are paving the way for the success of precision medicine for cancer patients, but inflammatory diseases have lagged behind in this respect. This review explores the current status of biomarker prediction for inflammatory diseases from within the FAC using omics technologies and highlights the benefits of future potential biomarker identification approaches.
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Affiliation(s)
- Johanne Brooks
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Alastair Watson
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom; Gastroenterology Department, Norfolk and Norwich University Hospital, Norwich NR4 7UY, United Kingdom
| | - Tamas Korcsmaros
- Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom.
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Wang J, Zhang C, Wu SG, Shang C, Huang L, Zhang T, Zhang W, Zhang Y, Zhang L. Additional Evidence Supports Association of Common Variants in COL11A1 with Increased Risk of Hip Osteoarthritis Susceptibility. Genet Test Mol Biomarkers 2016; 21:86-91. [PMID: 27936936 DOI: 10.1089/gtmb.2016.0308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE In a recent study single nucleotide polymorphisms (SNPs) in the COL11A1 gene were found to be associated with hip osteoarthritis (OA) among European populations. In this study, our aim was to identify common genetic variants in COL11A1 predisposing to primary hip OA in Han Chinese individuals. METHODS We designed a case-control study that included 313 hip OA patients and 911 unrelated healthy controls. Fourteen tagging single-nucleotide polymorphisms (SNPs) were genotyped, and single SNP and haplotypic association analyses were performed. RESULTS Two SNPs (rs1241164 and rs4907986) were found to be significantly associated with hip OA risk (adjusted p = 0.000731 and 0.000477). An increased risk of OA was associated with possession of the C allele of rs1241164 (adjusted odds ratio [OR] = 1.73, 95% confidence interval [CI] = 1.27-2.36) and the T allele of rs4907986 (adjusted OR = 1.72, 95% CI = 1.24-2.35). Similar results were confirmed via genotypic association analyses. Moreover, two different haplotype blocks, including rs1241164 and rs4907986, respectively, were found to be strongly associated with hip OA risk as well. CONCLUSION Variants in the COL11A1 gene modify individual susceptibility to hip OA in the Han Chinese population.
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Affiliation(s)
- Jinhua Wang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Chen Zhang
- 2 The First Department of Orthopedic, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Stephen G Wu
- 3 Department of Energy, Environment and Chemical Engineering, Washington University , Saint Louis, Missouri
| | - Chi Shang
- 4 Department of Hand Surgery, Honghui Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Lun Huang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Tong Zhang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Wen Zhang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Yanping Zhang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
| | - Lei Zhang
- 1 Department of Laboratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University , Xi'an, China
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