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Decreased mRNA expression level of FOXP3 correlate with TNF-α in peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis patients: a case control study. CURRENT ORTHOPAEDIC PRACTICE 2022. [DOI: 10.1097/bco.0000000000001067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Soremekun OS, Ezenwa C, Soliman M, Chikowore T, Nashiru O, Fatumo S. Transcription-translation error: In-silico investigation of the structural and functional impact of deleterious single nucleotide polymorphisms in GULP1 gene. INFORMATICS IN MEDICINE UNLOCKED 2020; 22:100503. [PMID: 33665355 PMCID: PMC7928429 DOI: 10.1016/j.imu.2020.100503] [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] [Indexed: 11/17/2022] Open
Abstract
Nonsynonymous single nucleotide polymorphisms (nsSNPs) are one of the most common forms of mutations known to disrupt the product of translation thereby altering the protein structure-function relationship. GULP1 (PTB domain-containing engulfment adaptor protein 1) is an evolutionarily conserved adaptor protein that has been associated with glycated hemoglobin (HbA1c) in Genome-Wide Association Studies (GWAS). In order to understand the role of GULP1 in the etiology of diabetes, it is important to study some functional nsSNPs present within the GULP1 protein. We, therefore, used a SNPinformatics approach to retrieve, classify, and determine the stability effect of some nsSNPs. Y27C, G142D, A144T, and Y149C were jointly predicted by the pathogenic-classifying tools to be disease-causing, however, only G142D, A144T, and Y149C had their structural architecture perturbed as predicted by I-MUTANT and MuPro. Interestingly, G142D and Y149C occur at positions 142 and 149 of GULP1 which coincidentally are found within the binding site of GULP1. Protein-Protein interaction analysis also revealed that GULP1 interacted with 10 proteins such as Cell division cycle 5-like protein (CDC5L), ADP-ribosylation factor 6 (ARF6), Arf-GAP with coiled-coil (ACAP1), and Multiple epidermal growth factor-like domains protein 10 (MEGF10), etc. Taken together, rs1357922096, rs1264999716, and rs128246649 could be used as genetic biomarkers for the diagnosis of diabetes. However, being a computational study, these nsSNPs require experimental validation to explore their metabolic involvement in the pathogenesis of diseases.
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Affiliation(s)
- Opeyemi S. Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
- The African Computational Genomics (TACG) Research Group, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Chisom Ezenwa
- Centre for Genomics Research and Innovation, National Biotechnology Agency, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Mahmoud Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Oyekanmi Nashiru
- Centre for Genomics Research and Innovation, National Biotechnology Agency, Abuja, Nigeria
| | - Segun Fatumo
- Centre for Genomics Research and Innovation, National Biotechnology Agency, Abuja, Nigeria
- The African Computational Genomics (TACG) Research Group, MRC/UVRI LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-communicable Disease Epidemiology (NCDE), London School of Hygiene and Tropical Medicine, London, United Kingdom
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Living on the Edge: Efferocytosis at the Interface of Homeostasis and Pathology. Immunity 2019; 50:1149-1162. [PMID: 31117011 DOI: 10.1016/j.immuni.2019.04.018] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Accepted: 04/29/2019] [Indexed: 01/23/2023]
Abstract
Nearly every tissue in the body undergoes routine turnover of cells as part of normal healthy living. The majority of these cells undergoing turnover die via apoptosis, and then are rapidly removed by phagocytes by the process of efferocytosis that is anti-inflammatory. However, a number of pathologies have recently been linked to defective clearance of apoptotic cells. Perturbed clearance arises for many reasons, including overwhelming of the clearance machinery, disruptions at different stages of efferocytosis, and responses of phagocytes during efferocytosis, all of which can alter the homeostatic tissue environment. This review covers linkages of molecules involved in the different phases of efferocytosis to disease pathologies that can arise due to their loss or altered function.
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Chen YJ, Chang WA, Wu LY, Huang CF, Chen CH, Kuo PL. Identification of Novel Genes in Osteoarthritic Fibroblast-Like Synoviocytes Using Next-Generation Sequencing and Bioinformatics Approaches. Int J Med Sci 2019; 16:1057-1071. [PMID: 31523167 PMCID: PMC6743272 DOI: 10.7150/ijms.35611] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/05/2019] [Indexed: 01/15/2023] Open
Abstract
Synovitis in osteoarthritis (OA) the consequence of low grade inflammatory process caused by cartilage breakdown products that stimulated the production of pro-inflammatory mediators by fibroblast-like synoviocytes (FLS). FLS participate in joint homeostasis and low grade inflammation in the joint microenvironment triggers FLS transformation. In the current study, we aimed to identify differentially expressed genes and potential miRNA regulations in human OA FLS through deep sequencing and bioinformatics approaches. The 245 differentially expressed genes in OA FLS were identified, and pathway analysis using various bioinformatics databases indicated their enrichment in functions related to altered extracellular matrix organization, cell adhesion and cellular movement. Moreover, among the 14 dysregulated genes with potential miRNA regulations identified, src kinase associated phosphoprotein 2 (SKAP2), adaptor related protein complex 1 sigma 2 subunit (AP1S2), PHD finger protein 21A (PHF21A), lipoma preferred partner (LPP), and transcription factor AP-2 alpha (TFAP2A) showed similar expression patterns in OA FLS and OA synovial tissue datasets in Gene Expression Omnibus database. Ingenuity Pathway Analysis identified the dysregulated LPP participated in cell migration and cell spreading of OA FLS, which was potentially regulated by miR-141-3p. The current findings suggested new perspectives into understanding the novel molecular signatures of FLS involved in the pathogenesis of OA, which may be potential therapeutic targets.
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Affiliation(s)
- Yi-Jen Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ching-Fen Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chia-Hsin Chen
- Department of Physical Medicine and Rehabilitation, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.,Department of Physical Medicine and Rehabilitation, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Orthopaedic Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Center for Cancer Research, Kaohsiung Medical University
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Datta S, Nam HS, Hayashi M, Maldonado L, Goldberg R, Brait M, Sidransky D, Illei P, Baras A, Vij N, Hoque MO. Expression of GULP1 in bronchial epithelium is associated with the progression of emphysema in chronic obstructive pulmonary disease. Respir Med 2017; 124:72-78. [DOI: 10.1016/j.rmed.2017.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 02/08/2017] [Accepted: 02/12/2017] [Indexed: 11/16/2022]
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Role of cysteine‑rich angiogenic inducer 61 in fibroblast‑like synovial cell proliferation and invasion in rheumatoid arthritis. Mol Med Rep 2014; 11:917-23. [PMID: 25351421 PMCID: PMC4262486 DOI: 10.3892/mmr.2014.2770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/08/2014] [Indexed: 02/07/2023] Open
Abstract
Cysteine-rich angiogenic inducer 61 (Cyr61) is a novel molecule that has been shown to be increased in the synovial tissues of patients with rheumatoid arthritis (RA). The present study was conducted in order to investigate the role of Cyr61 in the pathogenesis of RA. A human genome-wide gene assay was used to screen gene expression in synovial tissues obtained from four patients with RA and three patients with osteoarthritis (OA). To examine the role of Cyr61 in the phenotype of RA-fibroblast-like synovial (FLS) cells, Cyr61 expression in RA-FLS cells was knocked down using small interfering RNA (siRNA). Normal FLS cells transduced with lentiviral vectors encoding Cyr61 cDNA were used to further explore the effects of this molecule on FLS cell apoptosis, proliferation and invasion. The study found that the Cyr61 gene was highly expressed in the synovial cells from patients with RA compared with those from patients with OA. Downregulation of Cyr61 by siRNA led to impaired cell proliferation and invasion. Furthermore, it decreased the levels of matrix metalloproteinase (MMP)-3 and MMP-13, and induced apoptosis in RA-FLS cells. Conversely, overexpression of Cyr61 in normal FLS cells led to opposite effects. In conclusion, these results indicate that Cyr61 is capable of promoting RA-FLS cell proliferation and invasion via the suppression of apoptosis and the regulation of MMP expression. Therefore, Cyr61 may be a good target molecule for the treatment and prevention of RA.
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Toonen EJM, Gilissen C, Franke B, Kievit W, Eijsbouts AM, den Broeder AA, van Reijmersdal SV, Veltman JA, Scheffer H, Radstake TRDJ, van Riel PLCM, Barrera P, Coenen MJH. Validation study of existing gene expression signatures for anti-TNF treatment in patients with rheumatoid arthritis. PLoS One 2012; 7:e33199. [PMID: 22457743 PMCID: PMC3310059 DOI: 10.1371/journal.pone.0033199] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/06/2012] [Indexed: 12/28/2022] Open
Abstract
So far, there are no means of identifying rheumatoid arthritis (RA) patients who will fail to respond to tumour necrosis factor blocking agents (anti-TNF), prior to treatment. We set out to validate eight previously reported gene expression signatures predicting therapy outcome. Genome-wide expression profiling using Affymetrix GeneChip Exon 1.0 ST arrays was performed on RNA isolated from whole blood of 42 RA patients starting treatment with infliximab or adalimumab. Clinical response according to EULAR criteria was determined at week 14 of therapy. Genes that have been reported to be associated with anti-TNF treatment were extracted from our dataset. K-means partition clustering was performed to assess the predictive value of the gene-sets. We performed a hypothesis-driven analysis of the dataset using eight existing gene sets predictive of anti-TNF treatment outcome. The set that performed best reached a sensitivity of 71% and a specificity of 61%, for classifying the patients in the current study. We successfully validated one of eight previously reported predictive expression profile. This replicated expression signature is a good starting point for developing a prediction model for anti-TNF treatment outcome that can be used in a daily clinical setting. Our results confirm that gene expression profiling prior to treatment is a useful tool to predict anti-TNF (non) response.
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Affiliation(s)
- Erik J. M. Toonen
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Barbara Franke
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Wietske Kievit
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Agnes M. Eijsbouts
- Department of Rheumatology of the St Maartenskliniek, Nijmegen, The Netherlands
| | | | - Simon V. van Reijmersdal
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Joris A. Veltman
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Piet L. C. M. van Riel
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Pilar Barrera
- Department of Rheumatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Marieke J. H. Coenen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail:
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Lee HM, Sugino H, Aoki C, Shimaoka Y, Suzuki R, Ochi K, Ochi T, Nishimoto N. Abnormal networks of immune response-related molecules in bone marrow cells from patients with rheumatoid arthritis as revealed by DNA microarray analysis. Arthritis Res Ther 2011; 13:R89. [PMID: 21679443 PMCID: PMC3218904 DOI: 10.1186/ar3364] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 04/20/2011] [Accepted: 06/16/2011] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic synovitis that progresses to destruction of cartilage and bone. Bone marrow (BM) cells have been shown to contribute to this pathogenesis. In this study, we compared differentially expressed molecules in BM cells from RA and osteoarthritis (OA) patients and analyzed abnormal regulatory networks to identify the role of BM cells in RA. METHODS Gene expression profiles (GEPs) in BM-derived mononuclear cells from 9 RA and 10 OA patients were obtained by DNA microarray. Up- and down-regulated genes were identified by comparing the GEPs from the two patient groups. Bioinformatics was performed by Expression Analysis Systemic Explorer (EASE) 2.0 based on gene ontology, followed by network pathway analysis with Ingenuity Pathways Analysis (IPA) 7.5. RESULTS The BM mononuclear cells showed 764 up-regulated and 1,910 down-regulated genes in RA patients relative to the OA group. EASE revealed that the gene category response to external stimulus, which included the gene category immune response, was overrepresented by the up-regulated genes. So too were the gene categories signal transduction and phosphate metabolism. Down-regulated genes were dominantly classified in three gene categories: cell proliferation, which included mitotic cell cycle, DNA replication and chromosome cycle, and DNA metabolism. Most genes in these categories overlapped with each other. IPA analysis showed that the up-regulated genes in immune response were highly relevant to the antigen presentation pathway and to interferon signaling. The major histocompatibility complex (MHC) class I molecules, human leukocyte antigen (HLA)-E, HLA-F, and HLA-G, tapasin (TAP) and TAP binding protein, both of which are involved in peptide antigen binding and presentation via MHC class I molecules, are depicted in the immune response molecule networks. Interferon gamma and interleukin 8 were overexpressed and found to play central roles in these networks. CONCLUSIONS Abnormal regulatory networks in the immune response and cell cycle categories were identified in BM mononuclear cells from RA patients, indicating that the BM is pathologically involved in RA.
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Affiliation(s)
- Hooi-Ming Lee
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Hidehiko Sugino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita, Osaka 565-0871, Japan
| | - Chieko Aoki
- Laboratory of Immune Regulation, Wakayama Medical University, 105 Saito Bio Innovation Center, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | | | - Ryuji Suzuki
- Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, National Hospital Organization, 18-1 Sakuradai, Sagamihara, Kanagawa 252-0392, Japan
| | - Kensuke Ochi
- Kawasaki Municipal Kawasaki Hospital, 12-1 Shinkawa-dori, Kawasaki-ku, Kawasaki, Kanagawa 210-0013, Japan
| | - Takahiro Ochi
- Osaka Police Hospital, 10-31 Kitayama-chou, Tennoji-ku, Osaka 543-0035, Japan
| | - Norihiro Nishimoto
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita, Osaka 565-0871, Japan
- Laboratory of Immune Regulation, Wakayama Medical University, 105 Saito Bio Innovation Center, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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Elliott MR, Ravichandran KS. Clearance of apoptotic cells: implications in health and disease. ACTA ACUST UNITED AC 2010; 189:1059-70. [PMID: 20584912 PMCID: PMC2894449 DOI: 10.1083/jcb.201004096] [Citation(s) in RCA: 383] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Recent advances in defining the molecular signaling pathways that regulate the phagocytosis of apoptotic cells have improved our understanding of this complex and evolutionarily conserved process. Studies in mice and humans suggest that the prompt removal of dying cells is crucial for immune tolerance and tissue homeostasis. Failed or defective clearance has emerged as an important contributing factor to a range of disease processes. This review addresses how specific molecular alterations of engulfment pathways are linked to pathogenic states. A better understanding of the apoptotic cell clearance process in healthy and diseased states could offer new therapeutic strategies.
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Affiliation(s)
- Michael R Elliott
- Center for Cell Clearance and the Department of Microbiology, University of Virginia, Charlottesville, VA 22908, USA
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Wu G, Zhu L, Dent JE, Nardini C. A comprehensive molecular interaction map for rheumatoid arthritis. PLoS One 2010; 5:e10137. [PMID: 20419126 PMCID: PMC2855702 DOI: 10.1371/journal.pone.0010137] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 03/15/2010] [Indexed: 12/15/2022] Open
Abstract
Background Computational biology contributes to a variety of areas related to life sciences and, due to the growing impact of translational medicine - the scientific approach to medicine in tight relation with basic science -, it is becoming an important player in clinical-related areas. In this study, we use computation methods in order to improve our understanding of the complex interactions that occur between molecules related to Rheumatoid Arthritis (RA). Methodology Due to the complexity of the disease and the numerous molecular players involved, we devised a method to construct a systemic network of interactions of the processes ongoing in patients affected by RA. The network is based on high-throughput data, refined semi-automatically with carefully curated literature-based information. This global network has then been topologically analysed, as a whole and tissue-specifically, in order to translate the experimental molecular connections into topological motifs meaningful in the identification of tissue-specific markers and targets in the diagnosis, and possibly in the therapy, of RA. Significance We find that some nodes in the network that prove to be topologically important, in particular AKT2, IL6, MAPK1 and TP53, are also known to be associated with drugs used for the treatment of RA. Importantly, based on topological consideration, we are also able to suggest CRKL as a novel potentially relevant molecule for the diagnosis or treatment of RA. This type of finding proves the potential of in silico analyses able to produce highly refined hypotheses, based on vast experimental data, to be tested further and more efficiently. As research on RA is ongoing, the present map is in fieri, despite being -at the moment- a reflection of the state of the art. For this reason we make the network freely available in the standardised and easily exportable .xml CellDesigner format at ‘www.picb.ac.cn/ClinicalGenomicNTW/temp.html’ and ‘www.celldesigner.org’.
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Affiliation(s)
- Gang Wu
- Group of Clinical Genomic Networks, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Lisha Zhu
- Group of Clinical Genomic Networks, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jennifer E. Dent
- Group of Clinical Genomic Networks, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Christine Nardini
- Group of Clinical Genomic Networks, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
- * E-mail:
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Lequerré T, Bansard C, Vittecoq O, Derambure C, Hiron M, Daveau M, Tron F, Ayral X, Biga N, Auquit-Auckbur I, Chiocchia G, Le Loët X, Salier JP. Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia. Arthritis Res Ther 2009; 11:R99. [PMID: 19563633 PMCID: PMC2714155 DOI: 10.1186/ar2744] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2009] [Revised: 06/09/2009] [Accepted: 06/29/2009] [Indexed: 11/16/2022] Open
Abstract
Introduction Rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms are still poorly understood. Because previous microarray studies have only focused on long-standing (LS) RA compared to osteoarthritis, we aimed to compare the molecular profiles of early and LS RA versus control synovia. Methods Synovial biopsies were obtained by arthroscopy from 15 patients (4 early untreated RA, 4 treated LS RA and 7 controls, who had traumatic or mechanical lesions). Extracted mRNAs were used for large-scale gene-expression profiling. The different gene-expression combinations identified by comparison of profiles of early, LS RA and healthy synovia were linked to the biological processes involved in each situation. Results Three combinations of 719, 116 and 52 transcripts discriminated, respectively, early from LS RA, and early or LS RA from healthy synovia. We identified several gene clusters and distinct molecular signatures specifically expressed during early or LS RA, thereby suggesting the involvement of different pathophysiological mechanisms during the course of RA. Conclusions Early and LS RA have distinct molecular signatures with different biological processes participating at different times during the course of the disease. These results suggest that better knowledge of the main biological processes involved at a given RA stage might help to choose the most appropriate treatment.
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Affiliation(s)
- Thierry Lequerré
- Department of Rheumatology, Rouen University Hospital and Inserm 905 & Institut Fédératif de Recherche Multidisciplinaire sur les Peptides 23, Institute for Biomedical Research, University of Rouen, 76031 Rouen Cedex, France.
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Junta CM, Sandrin-Garcia P, Fachin-Saltoratto AL, Mello SS, Oliveira RDR, Rassi DM, Giuliatti S, Sakamoto-Hojo ET, Louzada-Junior P, Donadi EA, Passos GAS. Differential gene expression of peripheral blood mononuclear cells from rheumatoid arthritis patients may discriminate immunogenetic, pathogenic and treatment features. Immunology 2008; 127:365-72. [PMID: 19191904 DOI: 10.1111/j.1365-2567.2008.03005.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
This study aimed to evaluate the association between the differential gene expression profiling of peripheral blood mononuclear cells of rheumatoid arthritis patients with their immunogenetic (human leucocyte antigen shared-epitope, HLA-SE), autoimmune response [anti-cyclic citrullinated peptide (CCP) antibodies], disease activity score (DAS-28) and treatment (disease-modifying antirheumatic drugs and tumour necrosis factor blocker) features. Total RNA samples were copied into Cy3-labelled complementary DNA probes, hybridized onto a glass slide microarray containing 4500 human IMAGE complementary DNA target sequences. The Cy3-monocolour microarray images from patients were quantified and normalized. Analysis of the data using the significance analysis of microarrays algorithm together with a Venn diagram allowed the identification of shared and of exclusively modulated genes, according to patient features. Thirteen genes were exclusively associated with the presence of HLA-SE alleles, whose major biological function was related to signal transduction, phosphorylation and apoptosis. Ninety-one genes were associated with disease activity, being involved in signal transduction, apoptosis, response to stress and DNA damage. One hundred and one genes were associated with the presence of anti-CCP antibodies, being involved in signal transduction, cell proliferation and apoptosis. Twenty-eight genes were associated with tumour necrosis factor blocker treatment, being involved in intracellular signalling cascade, phosphorylation and protein transport. Some of these genes had been previously associated with rheumatoid arthritis pathogenesis, whereas others were unveiled for future research.
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Affiliation(s)
- Cristina Moraes Junta
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of São Paulo
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