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Giriyappagoudar M, Vastrad B, Horakeri R, Vastrad C. Study on Potential Differentially Expressed Genes in Idiopathic Pulmonary Fibrosis by Bioinformatics and Next-Generation Sequencing Data Analysis. Biomedicines 2023; 11:3109. [PMID: 38137330 PMCID: PMC10740779 DOI: 10.3390/biomedicines11123109] [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: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/24/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease with reduced quality of life and earlier mortality, but its pathogenesis and key genes are still unclear. In this investigation, bioinformatics was used to deeply analyze the pathogenesis of IPF and related key genes, so as to investigate the potential molecular pathogenesis of IPF and provide guidance for clinical treatment. Next-generation sequencing dataset GSE213001 was obtained from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified between IPF and normal control group. The DEGs between IPF and normal control group were screened with the DESeq2 package of R language. The Gene Ontology (GO) and REACTOME pathway enrichment analyses of the DEGs were performed. Using the g:Profiler, the function and pathway enrichment analyses of DEGs were performed. Then, a protein-protein interaction (PPI) network was constructed via the Integrated Interactions Database (IID) database. Cytoscape with Network Analyzer was used to identify the hub genes. miRNet and NetworkAnalyst databaseswereused to construct the targeted microRNAs (miRNAs), transcription factors (TFs), and small drug molecules. Finally, receiver operating characteristic (ROC) curve analysis was used to validate the hub genes. A total of 958 DEGs were screened out in this study, including 479 up regulated genes and 479 down regulated genes. Most of the DEGs were significantly enriched in response to stimulus, GPCR ligand binding, microtubule-based process, and defective GALNT3 causes HFTC. In combination with the results of the PPI network, miRNA-hub gene regulatory network and TF-hub gene regulatory network, hub genes including LRRK2, BMI1, EBP, MNDA, KBTBD7, KRT15, OTX1, TEKT4, SPAG8, and EFHC2 were selected. Cyclothiazide and rotigotinethe are predicted small drug molecules for IPF treatment. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of IPF, and provide a novel strategy for clinical therapy.
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Affiliation(s)
- Muttanagouda Giriyappagoudar
- Department of Radiation Oncology, Karnataka Institute of Medical Sciences (KIMS), Hubballi 580022, Karnataka, India;
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. Socitey’s College of Pharmacy, Gadag 582101, Karnataka, India;
| | - Rajeshwari Horakeri
- Department of Computer Science, Govt First Grade College, Hubballi 580032, Karnataka, India;
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India
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2
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Laigle L, Chadli L, Moingeon P. Biomarker-driven development of new therapies for autoimmune diseases: current status and future promises. Expert Rev Clin Immunol 2023; 19:305-314. [PMID: 36680799 DOI: 10.1080/1744666x.2023.2172404] [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] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Auto-immune diseases are complex and heterogeneous. Various types of biomarkers can be used to support precision medicine approaches to autoimmune diseases, ensuring that the right patient receives the most appropriate therapy to improve treatment outcomes. AREAS COVERED We review the recent progress made in modeling several autoimmune diseases such as Systemic Lupus Erythematosus, primary Sjogren Syndrome, and Rheumatoid Arthritis following extensive molecular profiling of large cohorts of patients. From this knowledge, BMKs are being identified which support diagnostic as well as patient stratification and prediction of response to treatment. The identification of biomarkers should be initiated early in drug development and properly validated during subsequent clinical trials. To ensure the robustness and reproducibility of biomarkers, the PERMIT Consortium recently established recommendations highlighting the importance of relevant study design, sample size, and appropriate validation of analytical methods. EXPERT OPINION The integration by AI-powered analytics of massive data provided by multi-omics technologies, high-resolution medical imaging and sensors borne by patients will eventually allow the identification of clinically relevant BMKs, likely in the form of combinatorial predictive algorithms, to support future drug development for autoimmune diseases.
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Affiliation(s)
| | - Loubna Chadli
- Servier Médical, Research and Development, Suresnes, France
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3
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Leone GM, Mangano K, Petralia MC, Nicoletti F, Fagone P. Past, Present and (Foreseeable) Future of Biological Anti-TNF Alpha Therapy. J Clin Med 2023; 12:jcm12041630. [PMID: 36836166 PMCID: PMC9963154 DOI: 10.3390/jcm12041630] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Due to the key role of tumor necrosis factor-alpha (TNF-α) in the pathogenesis of immunoinflammatory diseases, TNF-α inhibitors have been successfully developed and used in the clinical treatment of autoimmune disorders. Currently, five anti-TNF-α drugs have been approved: infliximab, adalimumab, golimumab, certolizumab pegol and etanercept. Anti-TNF-α biosimilars are also available for clinical use. Here, we will review the historical development as well as the present and potential future applications of anti-TNF-α therapies, which have led to major improvements for patients with several autoimmune diseases, such as rheumatoid arthritis (RA), ankylosing spondylitis (AS), Crohn's disease (CD), ulcerative colitis (UC), psoriasis (PS) and chronic endogenous uveitis. Other therapeutic areas are under evaluation, including viral infections, e.g., COVID-19, as well as chronic neuropsychiatric disorders and certain forms of cancer. The search for biomarkers able to predict responsiveness to anti-TNF-α drugs is also discussed.
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Affiliation(s)
- Gian Marco Leone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95123 Catania, Italy
| | - Katia Mangano
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95123 Catania, Italy
| | - Maria Cristina Petralia
- Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95123 Catania, Italy
- Correspondence:
| | - Paolo Fagone
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via S. Sofia 97, 95123 Catania, Italy
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Gao W, Hou R, Chen Y, Wang X, Liu G, Hu W, Yao K, Hao Y. A Predictive Disease Risk Model for Ankylosing Spondylitis: Based on Integrated Bioinformatic Analysis and Identification of Potential Biomarkers Most Related to Immunity. Mediators Inflamm 2023; 2023:3220235. [PMID: 37152368 PMCID: PMC10159744 DOI: 10.1155/2023/3220235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/08/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Background The pathogenesis of ankylosing spondylitis (AS) is still not clear, and immune-related genes have not been systematically explored in AS. The purpose of this paper was to identify the potential early biomarkers most related to immunity in AS and develop a predictive disease risk model with bioinformatic methods and the Gene Expression Omnibus database (GEO) to improve diagnostic and therapeutic efficiency. Methods To identify differentially expressed genes and create a gene coexpression network between AS and healthy samples, we downloaded the AS-related datasets GSE25101 and GSE73754 from the GEO database and employed weighted gene coexpression network analysis (WGCNA). We used the GSVA, GSEABase, limma, ggpubr, and reshape2 packages to score immune data and investigated the links between immune cells and immunological functions by using single-sample gene set enrichment analysis (ssGSEA). The value of the core gene set and constructed model for early AS diagnosis was investigated by using receiver operating characteristic (ROC) curve analysis. Results Biological function and immune score analyses identified central genes related to immunity, key immune cells, key related pathways, gene modules, and the coexpression network in AS. Granulysin (GNLY), Granulysin (GZMK), CX3CR1, IL2RB, dysferlin (DYSF), and S100A12 may participate in AS development through NK cells, CD8+ T cells, Th1 cells, and other immune cells and represent potential biomarkers for the early diagnosis of AS occurrence and progression. Furthermore, the T cell coinhibitory pathway may be involved in AS pathogenesis. Conclusion The AS disease risk model constructed based on immune-related genes can guide clinical diagnosis and treatment and may help in the development of personalized immunotherapy.
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Affiliation(s)
- Wenxin Gao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Ruirui Hou
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Yungang Chen
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Xiaoying Wang
- Jinan Vocational College of Nursing, Jinan, Shandong Province, China
| | - Guoyan Liu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Wanli Hu
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Kang Yao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Yanke Hao
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
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5
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Roszkowski L, Jaszczyk B, Plebańczyk M, Ciechomska M. S100A8 and S100A12 Proteins as Biomarkers of High Disease Activity in Patients with Rheumatoid Arthritis That Can Be Regulated by Epigenetic Drugs. Int J Mol Sci 2022; 24:ijms24010710. [PMID: 36614150 PMCID: PMC9820830 DOI: 10.3390/ijms24010710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune chronic inflammatory disease that is still not well understood in terms of its pathogenesis and presents diagnostic and therapeutic challenges. Monocytes are key players in initiating and maintaining inflammation through the production of pro-inflammatory cytokines and S100 proteins in RA. This study aimed to test a specific DNA methylation inhibitor (RG108) and activator (budesonide) in the regulation of pro-inflammatory mediators-especially the S100 proteins. We also searched for new biomarkers of high disease activity in RA patients. RNA sequencing analysis of healthy controls (HCs) and RA monocytes was performed. Genes such as the S100 family, TNF, and IL-8 were validated by qRT-PCR following DNA-methylation-targeted drug treatment in a monocytic THP-1 cell line. The concentrations of the S100A8, S100A11, and S100A12 proteins in the sera and synovial fluids of RA patients were tested and correlated with clinical parameters. We demonstrated that RA monocytes had significantly increased levels of S100A8, S100A9, S100A11, S100A12, MYD88, JAK3, and IQGAP1 and decreased levels of IL10RA and TGIF1 transcripts. In addition, stimulation of THP-1 cells with budesonide statistically reduced the expression of the S100 family, IL-8, and TNF genes. In contrast, THP-1 cells treated with RG108 had increased levels of the S100 family and TNF genes. We also revealed a significant upregulation of S100A8, S100A11, and S100A12 in RA patients, especially in early RA compared to HC sera. In addition, protein levels of S100A8, S100A11, and S100A12 in RA synovial fluids compared to HC sera were significantly increased. Overall, our data suggest that the S100A8 and S100A12 proteins are strongly elevated during ongoing inflammation, so they could be used as a better biomarker of disease activity than CRP. Interestingly, epigenetic drugs can regulate these S100 proteins, suggesting their potential use in targeting RA inflammation.
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Affiliation(s)
- Leszek Roszkowski
- Department of Outpatient Clinics, National Institute of Geriatrics, Rheumatology and Rehabilitation (NIGRiR), 02-637 Warsaw, Poland
| | - Bożena Jaszczyk
- Department of Outpatient Clinics, National Institute of Geriatrics, Rheumatology and Rehabilitation (NIGRiR), 02-637 Warsaw, Poland
| | - Magdalena Plebańczyk
- Department of Pathophysiology and Immunology, National Institute of Geriatrics, Rheumatology and Rehabilitation (NIGRiR), 02-637 Warsaw, Poland
| | - Marzena Ciechomska
- Department of Pathophysiology and Immunology, National Institute of Geriatrics, Rheumatology and Rehabilitation (NIGRiR), 02-637 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-670-95-63
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Gene Ontology Analysis Highlights Biological Processes Influencing Non-Response to Anti-TNF Therapy in Rheumatoid Arthritis. Biomedicines 2022; 10:biomedicines10081808. [PMID: 36009355 PMCID: PMC9404936 DOI: 10.3390/biomedicines10081808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
Anti-TNF therapy has significantly improved disease control in rheumatoid arthritis, but a fraction of rheumatoid arthritis patients do not respond to anti-TNF therapy or lose response over time. Moreover, the mechanisms underlying non-response to anti-TNF therapy remain largely unknown. To date, many single biomarkers of response to anti-TNF therapy have been published but they have not yet been analyzed as a system of interacting nodes. The aim of our study is to systematically elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis using the gene ontologies of previously published predictive biomarkers. Gene networks were constructed based on published biomarkers and then enriched gene ontology terms were elucidated in subgroups using gene ontology software tools. Our results highlight the novel role of proteasome-mediated protein catabolic processes (p = 2.91 × 10−15) and plasma lipoproteins (p = 4.55 × 10−11) in anti-TNF therapy response. The results of our gene ontology analysis help elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis and encourage further study of the highlighted processes.
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CKS2 and S100A12: Two Novel Diagnostic Biomarkers for Rheumatoid Arthritis. DISEASE MARKERS 2022; 2022:2431976. [PMID: 35789606 PMCID: PMC9250429 DOI: 10.1155/2022/2431976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic systematicness autoimmunity disease with joint inflammation. RA etiology is still unknown. Early and exact diagnosing is still hard to reach. In the paper, we purposed to discover novel diagnosis biological marker for RA. Two open, usable gene expression profiles of human RA as well as controlled specimens (dataset GSE17755 as well as GSE93272) were downloaded from the GEO database. Differentially expressed genes (DEGs) were screened between 331 RA and 88 control samples. Functional enrichment analysis was applied to explore the possible function of DEGs. Expression levels as well as diagnosis values of biological marker in RA were further verified in our cohort by the use of RT-PCR and ROC assays. We identified 13 DEGs between RA samples and control samples. 13 DEGs were remarkably abundant in NF-kappa B signal pathway. Among the 13 DEGs, CKS2, S100A12, LY96, and ANXA3 exhibited a strong diagnostic ability in screening RA specimens from normal specimens using all AUC > 0.8. Moreover, we confirmed that the expression of CKS2 and S100A12 was distinctly upregulated in RA specimens contrasted to normal specimens. Overall, serum CKS2 and S100A12 could be used as novel diagnosis biological markers for RA patients.
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Wei K, Jiang P, Zhao J, Jin Y, Zhang R, Chang C, Xu L, Xu L, Shi Y, Guo S, He D. Biomarkers to Predict DMARDs Efficacy and Adverse Effect in Rheumatoid Arthritis. Front Immunol 2022; 13:865267. [PMID: 35418971 PMCID: PMC8995470 DOI: 10.3389/fimmu.2022.865267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 12/28/2022] Open
Abstract
Rheumatoid arthritis (RA), one of the most common immune system diseases, mainly affects middle-aged and elderly individuals and has a serious impact on the quality of life of patients. Pain and disability caused by RA are significant symptoms negatively affecting patients, and they are especially seen when inappropriate treatment is administered. Effective therapeutic strategies have evolved over the past few decades, with many new disease-modifying antirheumatic drugs (DMARDs) being used in the clinic. Owing to the breakthrough in the treatment of RA, the symptoms of patients who could not be treated effectively in the past few years have been relieved. However, some patients complain about symptoms that have not been reported, implying that there are still some limitations in the RA treatment and evaluation system. In recent years, biomarkers, an effective means of diagnosing and evaluating the condition of patients with RA, have gradually been used in clinical practice to evaluate the therapeutic effect of RA, which is constantly being improved for accurate application of treatment in patients with RA. In this article, we summarize a series of biomarkers that may be helpful in evaluating the therapeutic effect and improving the efficiency of clinical treatment for RA. These efforts may also encourage researchers to devote more time and resources to the study and application of biomarkers, resulting in a new evaluation system that will reduce the inappropriate use of DMARDs, as well as patients’ physical pain and financial burden.
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Affiliation(s)
- Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yehua Jin
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Runrun Zhang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China.,The Second Affiliated Hospital of the Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Cen Chang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Linshuai Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yiming Shi
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Shicheng Guo
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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Vittecoq O, Guillou C, Hardouin J, Gerard B, Berenbaum F, Constantin A, Rincheval N, Combe B, Lequerre T, Cosette P. Validation in the ESPOIR cohort of vitamin K-dependent protein S (PROS) as a potential biomarker capable of predicting response to the methotrexate/etanercept combination. Arthritis Res Ther 2022; 24:72. [PMID: 35313956 PMCID: PMC8935769 DOI: 10.1186/s13075-022-02762-5] [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: 01/24/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background To validate the ability of PROS (vitamin K-dependent protein S) and CO7 (complement component C7) to predict response to the methotrexate (MTX)/etanercept (ETA) combination in rheumatoid arthritis (RA) patients who received this therapeutic combination in a well-documented cohort. Method From the ESPOIR cohort, RA patients having received the MTX/ETA or MTX/adalimumab (ADA) combination as a first-line biologic treatment were included. Serum concentrations of PROS and CO7 were measured by ELISA prior to the initiation of ETA or ADA, at a time where the disease was active (DAS28 ESR > 3.2). The clinical efficacy (response/non-response) of both combinations has been evaluated after at least 6 months of treatment, according to the EULAR response criteria with some modifications. Results Thirty-two were treated by MTX/ETA; the numbers of responders and non-responders were 24 and 8, respectively. Thirty-three patients received the MTX/ADA combination; 27 and 5 patients were respectively responders and non-responders. While there were no differences for demographic, clinical, biological, and X-rays data, as well as for CO7, serum levels of PROS tended to be significantly higher in responders to the MTX/ETA combination (p = 0.08) while no difference was observed in the group receiving MTX/ADA. For PROS, the best concentration threshold to differentiate both groups was calculated at 40 μg/ml using ROC curve. The theranostic performances of PROS appeared better for the ETA/MTX combination. When considering the response to this combination, analysis of pooled data from ESPOIR and SATRAPE (initially used to validate PROS and CO7 as potential theranostic biomarkers) cohorts led to a higher theranostic value of PROS that became significant (p = 0.009). Conclusion PROS might be one candidate of a combination of biomarkers capable of predicting the response to MTX/ETA combination in RA patients refractory to MTX. Trial registration ClinicalTrials.gov identifiers: NCT03666091 and NCT00234234.
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Affiliation(s)
- Olivier Vittecoq
- Rouen University Hospital, Department of Rheumatology & CIC-CRB1404, Normandie Univ, UNIROUEN, F 76000, Rouen, France. .,Inserm 1234 (PANTHER), F76000, Rouen, France.
| | - Clément Guillou
- Normandie Univ, PISSARO Proteomics Facility, IRIB, 76130 Mont-Saint Aignan, France & PBS-UMR6270 CNRS, FR3038 CNRS, 76130, Mont-Saint Aignan, France
| | - Julie Hardouin
- Normandie Univ, PISSARO Proteomics Facility, IRIB, 76130 Mont-Saint Aignan, France & PBS-UMR6270 CNRS, FR3038 CNRS, 76130, Mont-Saint Aignan, France
| | - Baptiste Gerard
- Rouen University Hospital, Department of Rheumatology & CIC-CRB1404, Normandie Univ, UNIROUEN, F 76000, Rouen, France.,Inserm 1234 (PANTHER), F76000, Rouen, France
| | - Francis Berenbaum
- Department of Rheumatology, AP-HP Saint-Antoine Hospital, Sorbonne University, Inserm CRSA, Paris, France
| | - Arnaud Constantin
- Rheumatology Department, Toulouse University Hospital, UMR 1043 & Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Nathalie Rincheval
- Unit of Statistics, Institute of Clinical Research EA2415, Montpellier University, Montpellier, France
| | - Bernard Combe
- Rheumatology Department, CHU Montpellier, Montpellier University, Montpellier, France
| | - Thierry Lequerre
- Rouen University Hospital, Department of Rheumatology & CIC-CRB1404, Normandie Univ, UNIROUEN, F 76000, Rouen, France.,Inserm 1234 (PANTHER), F76000, Rouen, France
| | - Pascal Cosette
- Normandie Univ, PISSARO Proteomics Facility, IRIB, 76130 Mont-Saint Aignan, France & PBS-UMR6270 CNRS, FR3038 CNRS, 76130, Mont-Saint Aignan, France
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10
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Wu YY, Li XF, Wu S, Niu XN, Yin SQ, Huang C, Li J. Role of the S100 protein family in rheumatoid arthritis. Arthritis Res Ther 2022; 24:35. [PMID: 35101111 PMCID: PMC8802512 DOI: 10.1186/s13075-022-02727-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/16/2022] [Indexed: 12/14/2022] Open
Abstract
Rheumatoid arthritis is a chronic systemic autoimmune disease characterized by synovial hyperplasia, inflammatory cell infiltration, and proliferation of inflammatory tissue (angiogranuloma). The destruction of joints and surrounding tissues eventually causes joint deformities and dysfunction or even loss. The S100 protein family is one of the biggest subtribes in the calcium-binding protein family and has more than 20 members. The overexpression of most S100 proteins in rheumatoid arthritis is closely related to its pathogenesis. This paper reviews the relationship between S100 proteins and the occurrence and development of rheumatoid arthritis. It will provide insights into the development of new clinical diagnostic markers and therapeutic targets for rheumatoid arthritis.
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Affiliation(s)
- Yuan-Yuan Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Xiao-Feng Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.,Postdoctoral Station of Clinical Medicine of Anhui Medical University, Hefei, Anhui, China
| | - Sha Wu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Xue-Ni Niu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Su-Qin Yin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, 230032, China.
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11
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Chen R, Li L, Li C, Su Y, Zhang Y, Pang X, Zheng J, Zeng Z, Chen MH, Zhang S. Prealbumin and Retinol-Binding Protein 4: The Promising Inflammatory Biomarkers for Identifying Endoscopic Remission in Crohn's Disease. J Inflamm Res 2022; 14:7371-7379. [PMID: 34992423 PMCID: PMC8715867 DOI: 10.2147/jir.s343125] [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] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022] Open
Abstract
Objective Endoscopic remission is the primary therapeutic target and associated with clinical outcome in Crohn’s disease (CD). Non-invasive and accurate biomarkers are important in monitoring endoscopic remission frequently. Our study aimed at investigating the predictive capacity of prealbumin and retinol-binding protein 4 (RBP4) for identifying endoscopic remission. Methods From June 2018 to December 2020, 515 endoscopy procedures (332 in the training cohort and 183 in the validation cohort) were enrolled in this multicentre retrospective cohort study. Blood samples were collected for prealbumin or RBP4 testing with 7 days before the endoscopy. A simple Endoscopic Score for CD (SES-CD) was performed to evaluate endoscopic activity and defined endoscopic remission. The area under receiver operating characteristic curve (AUROC), sensitivity, specificity, positive predictive value and negative predictive value were performed to assess the predictive capacity of the biomarkers. Results Serum concentration of prealbumin and RBP4 was demonstrated to be higher in patients with endoscopic remission and significantly negatively correlated with SES-CD in the training cohort. The AUROC of prealbumin and specificity of prealbumin and RBP4 were larger than that of C-reactive protein in the training cohort and the validation cohort. The model combining prealbumin and faecal calprotectin had the largest AUROC (0.842 [95% CI: 0.775–0.908]). Furthermore, in both cohorts, prealbumin had a larger AUROC than C-reactive protein for identifying endoscopic remission in patients with anti-tumour necrosis factor therapy. Conclusion Prealbumin and RBP4 were promising biomarkers for identifying endoscopic remission, especially in patients with anti-tumour necrosis factor therapy.
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Affiliation(s)
- Rirong Chen
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Li Li
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chao Li
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yuhan Su
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yingfan Zhang
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Xiaobai Pang
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jieqi Zheng
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Zhirong Zeng
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Min-Hu Chen
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Shenghong Zhang
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
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12
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Chen J, Li S, Ge Y, Kang J, Liao JF, Du JF, Tian J, Xie X, Li F. iTRAQ and PRM-Based Proteomic Analysis Provides New Insights into Mechanisms of Response to Triple Therapy in Patients with Rheumatoid Arthritis. J Inflamm Res 2021; 14:6993-7006. [PMID: 34955646 PMCID: PMC8694403 DOI: 10.2147/jir.s340351] [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: 09/28/2021] [Accepted: 12/08/2021] [Indexed: 12/29/2022] Open
Abstract
Background Approximately 30% of patients with rheumatoid arthritis (RA) respond poorly to combination therapy of multiple drugs. The molecular mechanisms of different responses to methotrexate + leflunomide + infliximab therapy in patients with RA were explored in this study. Methods Infliximab was administered to patients with RA whose disease activity score was higher than 5.1 after 1 month of combination therapy with methotrexate and leflunomide. After 14 weeks of undergoing triple therapy, patients with RA were classified as responders and non-responders. Protein profiles at baseline and 14th week were investigated via isobaric tags for relative and absolute quantification (iTRAQ), and proteins with significant differences ≥1.2 folds change or ≤0.8 folds change were defined as differentially expressed proteins (DEPs). Overlapping DEPs between responders and non-responders were confirmed by parallel reaction monitoring (PRM). Bioinformatic analyses were performed for DEPs. Results The results revealed 5 non-responders (NRs) and 15 responders (Rs). iTRAQ analysis indicated 13 overlapping DEPs and included 6 opposite change DEPs such as testicular tissue protein Li 70, cofilin 1, fibrinogen beta chain, galectin-10, serotransferrin (TF) and albumin. The difference in serotransferrin between responders and non-responders confirmed by PRM was significant. Verification by PRM indicated that TF was elevated in the Rs group and was reduced in the NRs group. Bioinformatic analysis indicated that serotransferrin was involved in the hypoxia-inducible factor-1 pathway and ferroptosis. Conclusion Serotransferrin-related molecular mechanism may be a new direction to study refractory RA.
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Affiliation(s)
- Jian Chen
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Shu Li
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Yan Ge
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Jin Kang
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Jia-Fen Liao
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Jin-Feng Du
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Jing Tian
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Xi Xie
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
| | - Fen Li
- Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, People's Republic of China
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13
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Bergman MJ, Kivitz AJ, Pappas DA, Kremer JM, Zhang L, Jeter A, Withers JB. Clinical Utility and Cost Savings in Predicting Inadequate Response to Anti-TNF Therapies in Rheumatoid Arthritis. Rheumatol Ther 2020; 7:775-792. [PMID: 32797404 PMCID: PMC7695768 DOI: 10.1007/s40744-020-00226-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
INTRODUCTION The PrismRA® test identifies rheumatoid arthritis (RA) patients who are unlikely to respond to anti-tumor necrosis factor (anti-TNF) therapies. This study evaluated the clinical and financial outcomes of incorporating PrismRA into routine clinical care of RA patients. METHODS A decision-analytic model was created to evaluate clinical and economic outcomes in the 12-month period following first biologic treatment. Two treatment strategies were compared: (1) observed clinical decision-making based on a 175-patient cohort receiving an anti-TNF therapy as their first biologic after failure of conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) and (2) modeled clinical decision-making of the same population using PrismRA results to inform first-line biologic treatment choice. Modeled costs include biologic drug pharmacy, non-biologic pharmacy, and total medical costs. The odds of inadequate response to anti-TNF therapies and various components of patient care were calculated based on PrismRA results. RESULTS Identifying predicted inadequate responders to anti-TNF therapies resulted in a modeled 38% increase in ACR50 response to first-line biologic therapies. The fraction of patients who achieved an ACR50 response to any therapy (TNFi and others) within the 12-month period was 33% higher in the PrismRA-stratified population than in the unstratified population (59 vs. 44%, respectively). When therapy prescriptions were modeled according to PrismRA results, cost savings were modeled for all financial variables: overall costs (4% decreased total, 19% decreased on ineffective treatments), total biologic drug pharmacy (4% total, 23% ineffective), non-biologic pharmacy (2% total, 19% ineffective), and medical costs (6% total, 19% ineffective). Female sex was the clinical metric that showed the greatest association with inadequate response to anti-TNF therapies (odds ratio 2.42, 95% confidence interval 1.20, 4.88). CONCLUSIONS If PrismRA is implemented into routine clinical care as modeled, predicting which RA patients will have an inadequate response to anti-TNF therapies could save > $7 million in overall ineffective healthcare costs per 1000 patients tested and increase targeted DMARD response rates in RA.
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Affiliation(s)
| | - Alan J Kivitz
- Department of Rheumatology, Altoona Center for Clinical Research, Duncansville, PA, USA
| | - Dimitrios A Pappas
- Columbia University, New York, NY, 10027, USA
- CORRONA, LCC, Waltham, MA, USA
| | - Joel M Kremer
- The Center for Rheumatology, Albany Medical College, Albany, NY, USA
| | - Lixia Zhang
- Scipher Medicine Corporation, 221 Crescent St., Suite 103A, Waltham, MA, USA
| | - Anna Jeter
- Scipher Medicine Corporation, 221 Crescent St., Suite 103A, Waltham, MA, USA
| | - Johanna B Withers
- Scipher Medicine Corporation, 221 Crescent St., Suite 103A, Waltham, MA, USA.
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Freites-Núñez D, Baillet A, Rodriguez-Rodriguez L, Nguyen MVC, Gonzalez I, Pablos JL, Balsa A, Vazquez M, Gaudin P, Fernandez-Gutierrez B. Efficacy, safety and cost-effectiveness of a web-based platform delivering the results of a biomarker-based predictive model of biotherapy response for rheumatoid arthritis patients: a protocol for a randomized multicenter single-blind active controlled clinical trial (PREDIRA). Trials 2020; 21:755. [PMID: 32867830 PMCID: PMC7456748 DOI: 10.1186/s13063-020-04683-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 08/14/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is one of the leading chronic inflammatory rheumatism. First-line therapy with synthetic disease-modifying antirheumatic drugs (sDMARD) is insufficiently effective in 40% of cases and these patients are treated with biotherapies. The increased use of these drugs each year is becoming a public health issue with considerable economic burden. This cost is 20 times higher than that of sDMARD. However, among patients treated with biotherapies, clinical practice shows that about one third will not respond to the selected drug. In nonresponse cases, practitioners currently have no choice but to perform an empirical switching between different treatments, because no tool capable of predicting the response or nonresponse to these molecules is currently available. METHODS The study is a prospective, phase III, controlled, multicenter, and randomized, single-blind (patient) clinical trial, including RA patients with a previous failure to anti-TNF therapies. The main objective is the analysis of the clinical and pharmacoeconomic impact after 6 months of treatment. Intervention arm: prescription of biotherapy (rituximab, adalimumab, abatacept) using SinnoTest® software, a prediction software based on proteomic biomarkers. Control arm: prescription of biotherapy based on current practice, without the SinnoTest® software (any biotherapy). In addition, a substudy will be carried out within this trial to generate a biobank and further analyze the proteomic profile of the patients and their modification throughout the study. DISCUSSION This clinical trial study will be the first validation study of a biotherapy response prediction software, bringing personalized medicine into the management of RA. We expect that the findings from this study will bring several benefits for the patient and the Health Care System. TRIAL REGISTRATION ClincalTrials.gov NCT04147026 . Registered on 31 October, 2019.
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Affiliation(s)
- Dalifer Freites-Núñez
- Rheumatology Department and Health Research Institute, Hospital Clinico San Carlos, Madrid, Spain
| | - Athan Baillet
- Department of Rheumatology, CHU Grenoble, Échirolles, France
| | - Luis Rodriguez-Rodriguez
- Rheumatology Department and Health Research Institute, Hospital Clinico San Carlos, Madrid, Spain.
| | | | - Isidoro Gonzalez
- Rheumatology Department and Health Research Institute, Hospital Universitario La Princesa, Madrid, Spain
| | - Jose Luis Pablos
- Rheumatology Department and Health Research Institute, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Alejandro Balsa
- Rheumatology Department and Health Research Institute, Hospital Universitario La Paz, Madrid, Spain
| | - Monica Vazquez
- Rheumatology Department and Health Research Institute, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Philippe Gaudin
- Department of Rheumatology, CHU Grenoble, Échirolles, France
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15
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Bon L, Scharl S, Vavricka S, Rogler G, Fournier N, Pittet V, Scharl M, Greuter T, Schreiner P, Frei P, Misselwitz B, Biedermann L, Zeitz J. Association of IBD specific treatment and prevalence of pain in the Swiss IBD cohort study. PLoS One 2019; 14:e0215738. [PMID: 31022217 PMCID: PMC6483222 DOI: 10.1371/journal.pone.0215738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/08/2019] [Indexed: 01/06/2023] Open
Abstract
Background Extraintestinal manifestations (EIM) contribute significantly to the burden of disease in inflammatory bowel disease (IBD). Pain is a leading symptom in IBD and could be seen as an EIM itself. Treatment of IBD associated pain is challenging and insufficiently studied. A better knowledge on the association of pain and IBD specific treatment is warranted to improve the management of IBD patients. Methods All patients of the Swiss IBD Cohort Study (SIBDCS) (n = 2152) received a questionnaire regarding pain localization, pain character, and the use of IBD specific medication. Results 1263 completed questionnaires were received. Twenty-one out of 184 patients (10%) receiving anti-TNF treatment compared to 142 out of 678 patients (21%) not receiving anti-TNF medication reported elbow pain (p = 0.002) while 28 out of 198 patients (14%) receiving steroid treatment significantly more often reported elbow pain compared to 59 from 696 patients (8%) not receiving steroids (p = 0.021). Furthermore, we found significantly more female patients under anti-TNF treatment to report knee/ lower leg pain and ankle/ foot pain compared to their male counterparts (36% vs. 20% and 22% vs. 10%, respectively, p = 0.015 for both comparisons). The frequency of knee, lower leg, ankle and foot pain was especially low in male patients under anti-TNF treatment, indicating a high benefit of male patients from anti-TNF therapy regarding EIM. Conclusions The frequency of elbow pain was lower in IBD patients treated with anti-TNF but higher in patients treated with steroids.
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Affiliation(s)
- Lorenz Bon
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sylvie Scharl
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stephan Vavricka
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Gerhard Rogler
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Fournier
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Valerie Pittet
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Michael Scharl
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Institute of Social and Preventive Medicine, University of Lausanne, Lausanne, Switzerland
| | - Thomas Greuter
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Schreiner
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Pascal Frei
- Gastroenterology Bethanien, Zurich, Switzerland
| | - Benjamin Misselwitz
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luc Biedermann
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jonas Zeitz
- Division of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Center of Gastroenterology, Clinic Hirslanden, Zurich, Switzerland
- * E-mail:
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