1
|
Assadiasl S, Rajabinejad M, Soleimanifar N, Makiyan F, Azizi E, Rezaiemanesh A, Nicknam MH. MicroRNAs-mediated regulation pathways in rheumatic diseases. Inflammopharmacology 2023; 31:129-144. [PMID: 36469219 DOI: 10.1007/s10787-022-01097-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 10/29/2022] [Indexed: 12/09/2022]
Abstract
Rheumatoid arthritis (RA) and ankylosing spondylitis (AS) are two common rheumatic disorders marked by persistent inflammatory joint disease. Patients with RA have osteodestructive symptoms, but those with AS have osteoproliferative manifestations. Ligaments, joints, tendons, bones, and muscles are all affected by rheumatic disorders. In recent years, many epigenetic factors contributing to the pathogenesis of rheumatoid disorders have been studied. MicroRNAs (miRNAs) are small, non-coding RNA molecules implicated as potential therapeutic targets or biomarkers in rheumatic diseases. MiRNAs play a critical role in the modulation of bone homeostasis and joint remodeling by controlling fibroblast-like synoviocytes (FLSs), chondrocytes, and osteocytes. Several miRNAs have been shown to be dysregulated in rheumatic diseases, including miR-10a, 16, 17, 18a, 19, 20a, 21, 27a, 29a, 34a, 103a, 125b, 132, 137, 143, 145, 146a, 155, 192, 203, 221, 222, 301a, 346, and 548a.The major molecular pathways governed by miRNAs in these cells are Wnt, bone-morphogenic protein (BMP), nuclear factor (NF)-κB, receptor activator of NF-κB (RANK)-RANK ligand (RANKL), and macrophage colony-stimulating factor (M-CSF) receptor pathway. This review aimed to provide an overview of the most important signaling pathways controlled by miRNAs in rheumatic diseases.
Collapse
Affiliation(s)
- Sara Assadiasl
- Molecular Immunology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Misagh Rajabinejad
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Narjes Soleimanifar
- Molecular Immunology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farideh Makiyan
- Division of Nanobiotechnology, Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Esfandiar Azizi
- Department of Immunology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Alireza Rezaiemanesh
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Daneshgah Street, Shahid Shiroudi Boulevard, PO-Box: 6714869914, Bākhtarān, Iran.
| | | |
Collapse
|
2
|
Kang L, Dai C, Wang L, Pan X. Potential biomarkers that discriminate rheumatoid arthritis and osteoarthritis based on the analysis and validation of datasets. BMC Musculoskelet Disord 2022; 23:319. [PMID: 35379209 PMCID: PMC8978354 DOI: 10.1186/s12891-022-05277-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 03/28/2022] [Indexed: 02/05/2023] Open
Abstract
Background Rheumatoid arthritis (RA) and osteoarthritis (OA) share some similar arthritic symptoms, but different mechanisms underlie the pathogenesis of these two diseases. Analysis of differentially expressed molecules in rheumatoid arthritis and osteoarthritis may assist in improving diagnosis and treatment strategies in clinical practice. Methods Microarray and RNA-seq data were acquired from the gene expression omnibus database. Differentially expressed genes (DEGs) were identified using Bioconductor packages. Receiver operating characteristic curves were plotted to assess performance. Gene ontology enrichment analysis was conducted using the clusterProfiler application. During validation, synovial fluid was harvested from patients who had undergone in-hospital joint replacement, in which the expression of proteins was measured using enzyme-linked immunosorbent assays. Results Compared with OA samples, RA samples showed 14 genes to be upregulated and 3 to be downregulated. Gene ontology analysis indicated that DEGs principally included molecules responsible for the regulation of a synovial tissue inflammatory response. Seven genes displayed a good discriminatory power with an AUC higher than 0.90. ADAMDEC1 was the biomarker that most clearly discriminated RA from OA in the database, exhibiting an AUC of 0.999, a sensitivity of 100%, and a specificity of 97.8%. Following validation, the expression levels of ADAMDEC1 in the synovial fluid from RA patients were significantly higher than those in the synovial fluid from OA patients (P < 0.05). At the cut-off value of 1957 pg/mL, ADAMDEC1 expression in the synovial fluid discriminated RA from OA with an AUC of 0.951, a specificity of 88.6%, and a sensitivity of 92.9%. Conclusion The differential expression of genes in RA compared with OA indicates potential targets for molecular diagnosis and treatment. The presence of ADAMDEC1 in synovial fluid is a good biomarker of RA. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-022-05277-x.
Collapse
Affiliation(s)
- Le Kang
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Chengqian Dai
- Department of Orthopedics, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Lihong Wang
- Department of Orthopedics, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Xinling Pan
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China.
| |
Collapse
|
3
|
Qiu S, Munir A, Malik SI, Khan S, Hassan A. Identification of differentially expressed genes and pathways crosstalk analysis in Rheumatoid and Osteoarthritis using next-generation sequencing and protein-protein networks. Saudi J Biol Sci 2021; 28:4656-4663. [PMID: 34354452 PMCID: PMC8325051 DOI: 10.1016/j.sjbs.2021.04.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 12/29/2022] Open
Abstract
Osteoarthritis occurs when protective cartilage of bones worn out. Similarlty, cartilage damage occurs mainly in the pannus cartilage in rheumatoid arthritis. It is a potentially debilitating condition, affecting women two to three times more often than men. The cause and prognosis of rheumatoid and osteoarthritis are still poorly known. However, advances in the study of disease pathogenesis have encouraged the creation of new therapeutics with improved outcomes. The purpose of this study is to investigate the differentially expressed genes potentially involved in dysregulated rheumatoid arthritis (RA) and their association to other types of arthritis, including osteoarthritis (OA). Complete RNAs were isolated for RNA expression profiling using next-generation sequencing from human primary cultured normal and RA chondrocytes. From RNA sequencing results 250 differentially expressed genes were identified using bioinformatics analysis, of which 32 were found to be significantly playing role in RA pathogenesis and its associated diseases. Molecular ontologies of the identified genes showed they are connected to Innate immune response, Protein phosphorylation, Transcription initiation from RNA polymerase II promoter, Immune response, Neoplasms of bones, as well as osteorthritis, and Rheumatoid arthritis. Among the identified genes, TRAF1, TRAF2, BAMP, STX11, MEOX2, AES, REL, FHL3, PNMA1, SGTA, LZTS2, SIAH2, PNMA1, and TFCP2 were found to be highly enriched in the protein-protein interaction network. The significant cross talks were found in Hypertrophic cardiomyopathy, Small cell lung cancer, Proteasome, p53 signaling pathway, Arrhythmogenic right ventricular cardiomyopathy, Small cell lung cancer, SNARE interactions in vesicular transport, RIG-I-like receptor signaling pathway, and Hypertrophic cardiomyopathy pathways. The results offer new opportunities for target gene control in RA and OA cartilage destruction.
Collapse
Affiliation(s)
- Shenqiang Qiu
- Department of Hand and Foot Surgery, Shandong Provincial Hospital affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, Shandong Province 250021, PR China
| | - Anum Munir
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
| | - Shaukat Iqbal Malik
- Department of Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Sajid Khan
- Department of Bioinformatics, Govt. Postgraduate College Mandian, Abbottabad 22010, Pakistan
| | - Amjad Hassan
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, 22010 Abbottabad, Pakistan
| |
Collapse
|
4
|
Erusappan T, Kondapuram SK, Ekambaram SP, Coumar MS. Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach. J Mol Model 2021; 27:14. [PMID: 33403456 DOI: 10.1007/s00894-020-04651-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/16/2020] [Indexed: 11/30/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disorder that commonly affects multiple joints of the body. Currently, there is no permanent cure to the disease, but it can be managed with several potent drugs that cause serious side effects on prolonged use. Traditional remedies are considered promising for the treatment of several diseases, particularly chronic conditions, because they have lower side effects compared to synthetic drugs. In folklore, the rhizome of Alpinia calcarata Roscoe (Zingiberaceae) is used as a major ingredient of herbal formulations to treat RA. Phytoconstituents reported in A. calcarata rhizomes are diterpenoids, sesquiterpenoid, flavonoids, phytosterol, and volatile oils. The present study is intended to understand the molecular-level interaction of phytoconstituents present in A. calcarata rhizomes with RA molecular targets using computational approaches. A total of 30 phytoconstituents reported from the plant were used to carry out docking with 36 known targets of RA. Based on the docking results, 4 flavonoids were found to be strongly interacting with the RA targets. Further, molecular dynamics simulation confirmed stable interaction of quercetin with 6 targets (JAK3, SYK, MMP2, TLR8, IRAK1, and JAK1), galangin with 2 targets (IRAK1 and JAK1), and kaempferol (IRAK1) with one target of RA. Moreover, the presence of these three flavonoids was confirmed in the A. calcarata rhizome extract using LC-MS analysis. The computational study suggests that flavonoids present in A. calcarata rhizome may be responsible for RA modulatory activity. Particularly, quercetin and galangin could be potential development candidates for the treatment of RA. Investigation of Alpinia calcarata constituent interactions with molecular targets of rheumatoid arthritis: docking, molecular dynamics, and network approach.
Collapse
Affiliation(s)
- Thamizharasi Erusappan
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Sree Karani Kondapuram
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Sanmuga Priya Ekambaram
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology Campus, Anna University, Tiruchirappalli, Tamil Nadu, 620 024, India.
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, 605014, India.
| |
Collapse
|
5
|
Xu Z, Li J, Yang H, Jiang L, Zhou X, Huang Y, Xu N. Association of CCL2 Gene Variants with Osteoarthritis. Arch Med Res 2019; 50:86-90. [PMID: 31495394 DOI: 10.1016/j.arcmed.2019.05.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/31/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The chemokine (C-C motif) Ligand 2 (CCL2)/CCR2 signaling was associated with macrophage accumulation, synovitis and cartilage damage in a mouse osteoarthritis (OA) model. MATERIALS AND METHODS Here a case-control study in a Chinese Han population was conducted to investigate the possible association between the CCL2 gene polymorphism and risk of OA. DNA was extracted from 367 primary knee OA patients and 303 healthy controls. Then CCL2 gene polymorphisms were determined using a standard polymerase chain reaction restriction fragment length polymorphism. Plasma CCL2 levels were measured by using sandwich enzyme-linked immunosorbent assay (ELISA). RESULTS It was found the CCL2 gene rs1024611 and rs4586 polymorphisms significantly increased the risk of OA. Stratified analyses showed the risk of OA might be increased by rs1024611 polymorphism in males and non-drinkers, and was increased by rs4586 polymorphism among smokers and drinkers. The CC genotype of rs4586 polymorphism was significantly correlated with the increased CCL2 level compared to TT genotype. CONCLUSIONS In conclusion, CCL2 gene polymorphisms (rs1024611 and rs4586) confer susceptibility to OA and may be potential markers for early diagnosis of OA.
Collapse
Affiliation(s)
- Zhonghua Xu
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China; Department of Orthopedics, Jintan Hospital Affiliated to Jiangsu Univeristy, Changzhou, China
| | - Jin Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing City, Zhejiang Province, China
| | - Haoyu Yang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Lifeng Jiang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xindie Zhou
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China.
| | - Yong Huang
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China.
| | - Nanwei Xu
- Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| |
Collapse
|
6
|
Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8340573. [PMID: 31139654 PMCID: PMC6500622 DOI: 10.1155/2019/8340573] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 01/06/2023]
Abstract
Background Osteoarthritis (OA) is the most common degenerative disease in orthopedics. However, the cause and underlying molecular mechanisms are not clear. This study aims to identify the hub genes and pathways involved in the occurrence of osteoarthritis. Methods The raw data of GSE89408 were downloaded from the Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) were identified by R software. The DAVID database was used for pathway and gene ontology analysis, and p<0.05 and gene count >2 were set as the cut-off point. Moreover, protein-protein interaction (PPI) network construction was applied for exploring the hub genes in osteoarthritis. The expression levels of the top ten hub genes in knee osteoarthritis synovial membranes and controls were detected by quantitative real-time PCR system. Results A total of 229 DEGs were identified in osteoarthritis synovial membranes compared with normal synovial membranes, including 145 upregulated and 84 downregulated differentially expressed genes. The KEGG pathway analysis results showed that up-DEGs were enriched in proteoglycans in cytokine-cytokine receptor interaction, chemokine signaling pathway, rheumatoid arthritis, and TNF signaling pathway, whereas down-DEGs were enriched in the PPAR signaling pathway and AMPK signaling pathway. The qRT-PCR results showed that the expression levels of ADIPOQ, IL6, and CXCR1 in the synovium of osteoarthritis were significantly increased (p <0.05).
Collapse
|
7
|
Sun D, Hu F, Gao H, Song Z, Xie W, Wang P, Shi L, Wang K, Li Y, Huang C, Li Z. Distribution of abnormal IgG glycosylation patterns from rheumatoid arthritis and osteoarthritis patients by MALDI-TOF-MSn. Analyst 2019; 144:2042-2051. [PMID: 30714583 DOI: 10.1039/c8an02014k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
IgG glycosylation differs in rheumatoid arthritis (RA) and osteoarthritis (OA), which should contribute to their pathogenesis research and diagnosis.
Collapse
|
8
|
Gabner S, Ertl R, Velde K, Renner M, Jenner F, Egerbacher M, Hlavaty J. Cytokine-induced interleukin-1 receptor antagonist protein expression in genetically engineered equine mesenchymal stem cells for osteoarthritis treatment. J Gene Med 2018; 20:e3021. [PMID: 29608232 PMCID: PMC6001542 DOI: 10.1002/jgm.3021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/23/2018] [Accepted: 03/24/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A combination of tissue engineering methods employing mesenchymal stem cells (MSCs) together with gene transfer takes advantage of innovative strategies and highlights a new approach for targeting osteoarthritis (OA) and other cartilage defects. Furthermore, the development of systems allowing tunable transgene expression as regulated by natural disease-induced substances is highly desirable. METHODS Bone marrow-derived equine MSCs were transduced with a lentiviral vector expressing interleukin-1 receptor antagonist (IL-1Ra) gene under the control of an inducible nuclear factor-kappa B-responsive promoter and IL-1Ra production upon pro-inflammatory cytokine stimulation [tumor necrosis factor (TNF)α, interleukin (IL)-1β] was analysed. To assess the biological activity of the IL-1Ra protein that was produced and the therapeutic effect of IL-1Ra-expressing MSCs (MSC/IL-1Ra), cytokine-based two- and three-dimensional in vitro models of osteoarthritis using equine chondrocytes were established and quantitative real-time polymerase chain reaction (PCR) analysis was used to measure the gene expression of aggrecan, collagen IIA1, interleukin-1β, interleukin-6, interleukin-8, matrix metalloproteinase-1 and matrix metalloproteinase-13. RESULTS A dose-dependent increase in IL-1Ra expression was found in MSC/IL-1Ra cells upon TNFα administration, whereas stimulation using IL-1β did not lead to IL-1Ra production above the basal level observed in nonstimulated cells as a result of the existing feedback loop. Repeated cycles of induction allowed on/off modulation of transgene expression. In vitro analyses revealed that IL-1Ra protein present in the conditioned medium from MSC/IL-1Ra cells blocks OA onset in cytokine-treated equine chondrocytes and co-cultivation of MSC/IL-1Ra cells with osteoarthritic spheroids alleviates the severity of the osteoarthritic changes. CONCLUSIONS Thus, pro-inflammatory cytokine induced IL-1Ra protein expression from genetically modified MSCs might represent a promising strategy for osteoarthritis treatment.
Collapse
Affiliation(s)
- Simone Gabner
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Reinhard Ertl
- VetCORE, Facility for ResearchUniversity of Veterinary MedicineViennaAustria
| | - Karsten Velde
- Equine University HospitalUniversity of Veterinary Medicine ViennaViennaAustria
| | - Matthias Renner
- Division of Medical BiotechnologyPaul‐Ehrlich‐InstitutLangenGermany
| | - Florien Jenner
- Equine University HospitalUniversity of Veterinary Medicine ViennaViennaAustria
| | - Monika Egerbacher
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
| | - Juraj Hlavaty
- Institute of Pathology and Forensic Veterinary Medicine, Working Group Histology and EmbryologyUniversity of Veterinary Medicine ViennaViennaAustria
| |
Collapse
|
9
|
Association of CCL13 levels in serum and synovial fluid with the radiographic severity of knee osteoarthritis. J Investig Med 2016; 63:545-7. [PMID: 25654294 DOI: 10.1097/jim.0000000000000150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVE CCL13, a recently identified CC chemokine, plays an important role in the process of joint destruction, which is considered a common cause for osteoarthritis (OA). This study aims to examine the relation of CCL13 levels in serum and synovial fluid (SF) with the radiographic severity of OA. METHODS CCL13 levels in serum and SF were evaluated using enzyme-linked immunosorbent assay method in 240 patients with knee OA and 134 control subjects. The progression of OA was classified using the Kellgren-Lawrence (KL) system by evaluating x-ray changes observed in anteroposterior knee radiography. RESULTS Knee OA patients had higher levels of serum CCL13 compared with control subjects. Knee OA patients with KL grade 4 showed significantly elevated CCL13 levels in serum and SF compared with those with KL grades 2 and 3. Knee OA patients with KL grade 3 had significantly higher SF levels of CCL13 compared with those with KL grade 2. CCL13 levels in serum and SF of knee OA patients were significantly correlated with disease severity evaluated by KL grading criteria. CONCLUSIONS CCL13 levels in serum and SF were correlated with the radiographic severity of OA. CCL13 levels in serum and SF may serve as a biomarker for the progression of OA.
Collapse
|
10
|
Sun ZL, Xu X, Zhou DP, Wang L, Wang FQ, Xu ZY, Ji W. Serum proteomic-based analysis by iTRAQ of damp-heat impeding syndrome of rheumatoid arthritis. Eur J Integr Med 2015. [DOI: 10.1016/j.eujim.2015.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
11
|
Liu T, Lin X, Yu H. Identifying genes related with rheumatoid arthritis via system biology analysis. Gene 2015; 571:97-106. [PMID: 26117171 DOI: 10.1016/j.gene.2015.06.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/18/2015] [Accepted: 06/21/2015] [Indexed: 01/04/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease that mainly attacks synovial joints. However, the underlying systematic relationship among different genes and biological processes involved in the pathogenesis are still unclear. By analyzing and comparing the transcriptional profiles from RA, OA (osteoarthritis) patients as well as ND (normal donors) with bioinformatics methods, we tend to uncover the potential molecular networks and critical genes which play important roles in RA and OA development. Initially, hierarchical clustering was performed to classify the overall transcriptional profiles. Differentially expressed genes (DEGs) between ND and RA and OA patients were identified. Furthermore, PPI networks were constructed, functional modules were extracted, and functional annotation was also applied. Our functional analysis identifies 22 biological processes and 2 KEGG pathways enriched in the commonly-regulated gene set. However, we found that number of set of genes differentially expressed genes only between RA and ND reaches up to 244, indicating this gene set may specifically accounts for processing to disease of RA. Additionally, 142 biological processes and 19 KEGG pathways are over-represented by these 244 genes. Meanwhile, although another 21 genes were differentially expressed only in OA and ND, no biological process nor pathway is over-represented by them.
Collapse
Affiliation(s)
- Tao Liu
- Department of Joint Surgery, affiliated Hospital of Binzhou Medical College, No. 661 Huanghe Er Road, Binzhou City, Shandong Province 256603, China.
| | - Xinmei Lin
- Department of Joint Surgery, affiliated Hospital of Binzhou Medical College, No. 661 Huanghe Er Road, Binzhou City, Shandong Province 256603, China.
| | - Hongjian Yu
- Department of Orthopaedics in Binzhou People Hospital, No. 515 Huanghe Qi Road, Binzhou City, Shandong Province 256603, China.
| |
Collapse
|
12
|
Wang K, Zhao L, Liu X, Hao Z, Zhou Y, Yang C, Li H. Differential co-expression analysis of rheumatoid arthritis with microarray data. Mol Med Rep 2014; 10:2421-6. [PMID: 25118911 DOI: 10.3892/mmr.2014.2491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 04/25/2014] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to investigate the underlying molecular mechanisms of rheumatoid arthritis (RA) using microarray expression profiles from osteoarthritis and RA patients, to improve diagnosis and treatment strategies for the condition. The gene expression profile of GSE27390 was downloaded from Gene Expression Omnibus, including 19 samples from patients with RA (n=9) or osteoarthritis (n=10). Firstly, the differentially expressed genes (DEGs) were obtained with the thresholds of |logFC|>1.0 and P<0.05, using the t‑test method in LIMMA package. Then, differentially co-expressed genes (DCGs) and differentially co-expressed links (DCLs) were screened with q<0.25 by the differential coexpression analysis and differential regulation analysis of gene expression microarray data package. Secondly, pathway enrichment analysis for DCGs was performed by the Database for Annotation, Visualization and Integrated Discovery and the DCLs associated with RA were selected by comparing the obtained DCLs with known transcription factor (TF)-targets in the TRANSFAC database. Finally, the obtained TFs were mapped to the known TF-targets to construct the network using cytoscape software. A total of 1755 DEGs, 457 DCGs and 101988 DCLs were achieved and there were 20 TFs in the obtained six TF-target relations (STAT3-TNF, PBX1‑PLAU, SOCS3-STAT3, GATA1-ETS2, ETS1-ICAM4 and CEBPE‑GATA1) and 457 DCGs. A number of TF-target relations in the constructed network were not within DCLs when the TF and target gene were DCGs. The identified TFs may have an important role in the pathogenesis of RA and have the potential to be used as biomarkers for the development of novel diagnostic and therapeutic strategies for RA.
Collapse
Affiliation(s)
- Kunpeng Wang
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Liqiang Zhao
- Department of Orthopedics, The Harbin Fifth Hospital, Harbin, Heilongjiang 150001, P.R. China
| | - Xuefeng Liu
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Zhenyong Hao
- Department of Orthopedics, The Harbin Fifth Hospital, Harbin, Heilongjiang 150001, P.R. China
| | - Yong Zhou
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Chuandong Yang
- Department of Orthopedics, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hongqiang Li
- Department of Orthopedics, The Harbin Fifth Hospital, Harbin, Heilongjiang 150001, P.R. China
| |
Collapse
|
13
|
Woetzel D, Huber R, Kupfer P, Pohlers D, Pfaff M, Driesch D, Häupl T, Koczan D, Stiehl P, Guthke R, Kinne RW. Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation. Arthritis Res Ther 2014; 16:R84. [PMID: 24690414 PMCID: PMC4060460 DOI: 10.1186/ar4526] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Discrimination of rheumatoid arthritis (RA) patients from patients with other inflammatory or degenerative joint diseases or healthy individuals purely on the basis of genes differentially expressed in high-throughput data has proven very difficult. Thus, the present study sought to achieve such discrimination by employing a novel unbiased approach using rule-based classifiers. METHODS Three multi-center genome-wide transcriptomic data sets (Affymetrix HG-U133 A/B) from a total of 79 individuals, including 20 healthy controls (control group - CG), as well as 26 osteoarthritis (OA) and 33 RA patients, were used to infer rule-based classifiers to discriminate the disease groups. The rules were ranked with respect to Kiendl's statistical relevance index, and the resulting rule set was optimized by pruning. The rule sets were inferred separately from data of one of three centers and applied to the two remaining centers for validation. All rules from the optimized rule sets of all centers were used to analyze their biological relevance applying the software Pathway Studio. RESULTS The optimized rule sets for the three centers contained a total of 29, 20, and 8 rules (including 10, 8, and 4 rules for 'RA'), respectively. The mean sensitivity for the prediction of RA based on six center-to-center tests was 96% (range 90% to 100%), that for OA 86% (range 40% to 100%). The mean specificity for RA prediction was 94% (range 80% to 100%), that for OA 96% (range 83.3% to 100%). The average overall accuracy of the three different rule-based classifiers was 91% (range 80% to 100%). Unbiased analyses by Pathway Studio of the gene sets obtained by discrimination of RA from OA and CG with rule-based classifiers resulted in the identification of the pathogenetically and/or therapeutically relevant interferon-gamma and GM-CSF pathways. CONCLUSION First-time application of rule-based classifiers for the discrimination of RA resulted in high performance, with means for all assessment parameters close to or higher than 90%. In addition, this unbiased, new approach resulted in the identification not only of pathways known to be critical to RA, but also of novel molecules such as serine/threonine kinase 10.
Collapse
Affiliation(s)
- Dirk Woetzel
- BioControl Jena GmbH, Wildenbruchstraße 15, 07745 Jena, Germany
| | - Rene Huber
- Experimental Rheumatology Unit, Department of Orthopedics, Jena University Hospital, Waldkrankenhaus Rudolf Elle, Klosterlausnitzer Straße 81, 07607 Eisenberg, Germany
- Institute of Clinical Chemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Peter Kupfer
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Dirk Pohlers
- Experimental Rheumatology Unit, Department of Orthopedics, Jena University Hospital, Waldkrankenhaus Rudolf Elle, Klosterlausnitzer Straße 81, 07607 Eisenberg, Germany
- Present address: Center of Diagnostics GmbH, Chemnitz Hospital, Flemmingstr. 2, 09116 Chemnitz, Germany
| | - Michael Pfaff
- BioControl Jena GmbH, Wildenbruchstraße 15, 07745 Jena, Germany
- Department of Medical Engineering and Biotechnology, University of Applied Sciences Jena, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Dominik Driesch
- BioControl Jena GmbH, Wildenbruchstraße 15, 07745 Jena, Germany
| | - Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charite-Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany
| | - Dirk Koczan
- Institute of Immunology, University of Rostock, Schillingallee 68, 18057 Rostock, Germany
| | - Peter Stiehl
- Institute of Pathology, University of Leipzig, Liebigstraße 24, 04103 Leipzig, Germany
| | - Reinhard Guthke
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Raimund W Kinne
- Experimental Rheumatology Unit, Department of Orthopedics, Jena University Hospital, Waldkrankenhaus Rudolf Elle, Klosterlausnitzer Straße 81, 07607 Eisenberg, Germany
| |
Collapse
|
14
|
Chang H, Docheva D, Knothe UR, Knothe Tate ML. Arthritic periosteal tissue from joint replacement surgery: a novel, autologous source of stem cells. Stem Cells Transl Med 2014; 3:308-17. [PMID: 24477075 PMCID: PMC3952924 DOI: 10.5966/sctm.2013-0056] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 11/14/2013] [Indexed: 12/17/2022] Open
Abstract
The overarching aim of this study is to assess the feasibility of using periosteal tissue from the femoral neck of arthritic hip joints, usually discarded in the normal course of hip replacement surgery, as an autologous source of stem cells. In addition, the study aims to characterize intrinsic differences between periosteum-derived cell (PDC) populations, isolated via either enzymatic digestion or a migration assay, including their proliferative capacity, surface marker expression, and multipotency, relative to commercially available human bone marrow-derived stromal cells (BMSCs) cultured under identical conditions. Commercial BMSCs and PDCs were characterized in vitro, using a growth assay, flow cytometry, as well as assay of Oil Red O, alizarin red, and Safranin O/Fast Green staining after respective culture in adipo-, osteo-, and chondrogenic media. Based on these outcome measures, PDCs exhibited proliferation rate, morphology, surface receptor expression, and multipotency similar to those of BMSCs. No significant correlation was observed between outcome measures and donor age or diagnosis (osteoarthritis [OA] and rheumatoid arthritis [RA], respectively), a profound finding given recent rheumatological studies indicating that OA and RA share not only common biomarkers and molecular mechanisms but also common pathophysiology, ultimately resulting in the need for joint replacement. Furthermore, PDCs isolated via enzymatic digestion and migration assay showed subtle differences in surface marker expression but otherwise no significant differences in proliferation or multipotency; the observed differences in surface marker expression may indicate potential effects of isolation method on the population of cells isolated and/or the behavior of the respective isolated cell populations. This study demonstrates, for the first time to our knowledge, the feasibility of using arthritic tissue resected during hip replacement as a source of autologous stem cells. In sum, periosteum tissue that is resected with the femoral neck in replacing the hip represents an unprecedented and, to date, unstudied source of stem cells from OA and RA patients. Follow-up studies will determine the degree to which this new, autologous source of stem cells can be banked for future use.
Collapse
|