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Sonomoto K, Fujino Y, Tanaka H, Nagayasu A, Nakayamada S, Tanaka Y. A Machine Learning Approach for Prediction of CDAI Remission with TNF Inhibitors: A Concept of Precision Medicine from the FIRST Registry. Rheumatol Ther 2024; 11:709-736. [PMID: 38637465 PMCID: PMC11111643 DOI: 10.1007/s40744-024-00668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
INTRODUCTION This study aimed to develop low-cost models using machine learning approaches predicting the achievement of Clinical Disease Activity Index (CDAI) remission 6 months after initiation of tumor necrosis factor inhibitors (TNFi) as primary biologic/targeted synthetic disease-modifying antirheumatic drugs (b/tsDMARDs) for rheumatoid arthritis (RA). METHODS Data of patients with RA initiating TNFi as first b/tsDMARD after unsuccessful methotrexate treatment were collected from the FIRST registry (August 2003 to October 2022). Baseline characteristics and 6-month CDAI were collected. The analysis used various machine learning approaches including logistic regression with stepwise variable selection, decision tree, support vector machine, and lasso logistic regression (Lasso), with 48 factors accessible in routine clinical practice for the prediction model. Robustness was ensured by k-fold cross validation. RESULTS Among the approaches tested, Lasso showed the advantages in predicting CDAI remission: with a mean area under the curve 0.704, sensitivity 61.7%, and specificity 69.9%. Predicted TNFi responders achieved CDAI remission at an average rate of 53.2%, while only 26.4% of predicted TNFi non-responders achieved remission. Encouragingly, the models generated relied solely on patient-reported outcomes and quantitative parameters, excluding subjective physician input. CONCLUSIONS While external cohort validation is warranted for broader applicability, this study highlights the potential for a low-cost predictive model to predict CDAI remission following TNFi treatment. The approach of the study using only baseline data and 6-month CDAI measures, suggests the feasibility of establishing regional cohorts to generate low-cost models tailored to specific regions or institutions. This may facilitate the application of regional/in-house precision medicine strategies in RA management.
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Affiliation(s)
- Koshiro Sonomoto
- Department of Clinical Nursing, School of Health Sciences, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Yoshihisa Fujino
- Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Atsushi Nagayasu
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Shingo Nakayamada
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, 1-1, Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
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Sharma SD, Bluett J. Towards Personalized Medicine in Rheumatoid Arthritis. Open Access Rheumatol 2024; 16:89-114. [PMID: 38779469 PMCID: PMC11110814 DOI: 10.2147/oarrr.s372610] [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: 01/04/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Rheumatoid arthritis (RA) is a chronic, incurable, multisystem, inflammatory disease characterized by synovitis and extra-articular features. Although several advanced therapies targeting inflammatory mechanisms underlying the disease are available, no advanced therapy is universally effective. Therefore, a ceiling of treatment response is currently accepted where no advanced therapy is superior to another. The current challenge for medical research is the discovery and integration of predictive markers of drug response that can be used to personalize medicine so that the patient is started on "the right drug at the right time". This review article summarizes our current understanding of predicting response to anti-rheumatic drugs in RA, obstacles impeding the development of personalized medicine approaches and future research priorities to overcome these barriers.
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Affiliation(s)
- Seema D Sharma
- Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - James Bluett
- Centre for Musculoskeletal Research, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
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Gerassy-Vainberg S, Starosvetsky E, Gaujoux R, Blatt A, Maimon N, Gorelik Y, Pressman S, Alpert A, Bar-Yoseph H, Dubovik T, Perets B, Katz A, Milman N, Segev M, Chowers Y, Shen-Orr SS. A personalized network framework reveals predictive axis of anti-TNF response across diseases. Cell Rep Med 2024; 5:101300. [PMID: 38118442 PMCID: PMC10829759 DOI: 10.1016/j.xcrm.2023.101300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/20/2023] [Accepted: 10/31/2023] [Indexed: 12/22/2023]
Abstract
Personalized treatment of complex diseases has been mostly predicated on biomarker identification of one drug-disease combination at a time. Here, we use a computational approach termed Disruption Networks to generate a data type, contextualized by cell-centered individual-level networks, that captures biology otherwise overlooked when performing standard statistics. This data type extends beyond the "feature level space", to the "relations space", by quantifying individual-level breaking or rewiring of cross-feature relations. Applying Disruption Networks to dissect high-dimensional blood data, we discover and validate that the RAC1-PAK1 axis is predictive of anti-TNF response in inflammatory bowel disease. Intermediate monocytes, which correlate with the inflammatory state, play a key role in the RAC1-PAK1 responses, supporting their modulation as a therapeutic target. This axis also predicts response in rheumatoid arthritis, validated in three public cohorts. Our findings support blood-based drug response diagnostics across immune-mediated diseases, implicating common mechanisms of non-response.
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Affiliation(s)
- Shiran Gerassy-Vainberg
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Elina Starosvetsky
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Renaud Gaujoux
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; CytoReason, Tel Aviv 67012, Israel
| | - Alexandra Blatt
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Naama Maimon
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Yuri Gorelik
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Sigal Pressman
- Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Ayelet Alpert
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Haggai Bar-Yoseph
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Tania Dubovik
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Benny Perets
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | | | - Neta Milman
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Meital Segev
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yehuda Chowers
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel; Department of Gastroenterology, Rambam Health Care Campus, Haifa 3109601, Israel; Clinical Research Institute, Rambam Health Care Campus, Haifa 3109601, Israel.
| | - Shai S Shen-Orr
- Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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Wang SS, Lewis MJ, Pitzalis C. DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis. Biomedicines 2023; 11:1987. [PMID: 37509625 PMCID: PMC10377185 DOI: 10.3390/biomedicines11071987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex condition that displays heterogeneity in disease severity and response to standard treatments between patients. Failure rates for conventional, target synthetic, and biologic disease-modifying rheumatic drugs (DMARDs) are significant. Although there are models for predicting patient response, they have limited accuracy, require replication/validation, or for samples to be obtained through a synovial biopsy. Thus, currently, there are no prediction methods approved for routine clinical use. Previous research has shown that genetics and environmental factors alone cannot explain the differences in response between patients. Recent studies have demonstrated that deoxyribonucleic acid (DNA) methylation plays an important role in the pathogenesis and disease progression of RA. Importantly, specific DNA methylation profiles associated with response to conventional, target synthetic, and biologic DMARDs have been found in the blood of RA patients and could potentially function as predictive biomarkers. This review will summarize and evaluate the evidence for DNA methylation signatures in treatment response mainly in blood but also learn from the progress made in the diseased tissue in cancer in comparison to RA and autoimmune diseases. We will discuss the benefits and challenges of using DNA methylation signatures as predictive markers and the potential for future progress in this area.
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Affiliation(s)
- Susan Siyu Wang
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
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Hedman ÅK, Winter E, Yoosuf N, Benita Y, Berg L, Brynedal B, Folkersen L, Klareskog L, Maciejewski M, Sirota-Madi A, Spector Y, Ziemek D, Padyukov L, Shen-Orr SS, Jelinsky SA. Peripheral blood cellular dynamics of rheumatoid arthritis treatment informs about efficacy of response to disease modifying drugs. Sci Rep 2023; 13:10058. [PMID: 37344505 DOI: 10.1038/s41598-023-36999-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by systemic inflammation and is mediated by multiple immune cell types. In this work, we aimed to determine the relevance of changes in cell proportions in peripheral blood mononuclear cells (PBMCs) during the development of disease and following treatment. Samples from healthy blood donors, newly diagnosed RA patients, and established RA patients that had an inadequate response to MTX and were about to start tumor necrosis factor inhibitors (TNFi) treatment were collected before and after 3 months of treatment. We used in parallel a computational deconvolution approach based on RNA expression and flow cytometry to determine the relative cell-type frequencies. Cell-type frequencies from deconvolution of gene expression indicate that monocytes (both classical and non-classical) and CD4+ cells (Th1 and Th2) were increased in RA patients compared to controls, while NK cells and B cells (naïve and mature) were significantly decreased in RA patients. Treatment with MTX caused a decrease in B cells (memory and plasma cell), and a decrease in CD4 Th cells (Th1 and Th17), while treatment with TNFi resulted in a significant increase in the population of B cells. Characterization of the RNA expression patterns found that most of the differentially expressed genes in RA subjects after treatment can be explained by changes in cell frequencies (98% and 74% respectively for MTX and TNFi).
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Affiliation(s)
- Åsa K Hedman
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Inflammation and Immunology, Pfizer, 1 Portland Street, Cambridge, MA, 02139, USA
| | | | - Niyaz Yoosuf
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Louise Berg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Boel Brynedal
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lasse Folkersen
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mateusz Maciejewski
- Department of Inflammation and Immunology, Pfizer, 1 Portland Street, Cambridge, MA, 02139, USA
| | | | | | - Daniel Ziemek
- Department of Inflammation and Immunology, Pfizer, Berlin, Germany
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shai S Shen-Orr
- CytoReason, Tel-Aviv, Israel
- Technion-Israel Institute of Technology, Haifa, Israel
| | - Scott A Jelinsky
- Department of Inflammation and Immunology, Pfizer, 1 Portland Street, Cambridge, MA, 02139, USA.
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Zhang S, Li P, Wu P, Yang L, Liu X, Liu J, Zhang Y, Zeng J. Predictors of response of rituximab in rheumatoid arthritis by weighted gene co-expression network analysis. Clin Rheumatol 2023; 42:529-538. [PMID: 36374432 DOI: 10.1007/s10067-022-06438-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/14/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE The purpose of this study was to identify a biomarker that can predict the efficacy of rituximab (RTX) in the treatment of rheumatoid arthritis (RA) patients. METHODS Utilized weighted gene co-expression network analysis (WGCNA) and LASSO regression analysis of whole blood transcriptome data (GSE15316 and GSE37107) related to RTX treatment for RA from the GEO database, the critical modules, and key genes related to the efficacy of RTX treatment for RA were found. The biological functions were further explored through enrichment analysis. The area under the ROC curve (AUC) was validated using the GSE54629 dataset. RESULTS WGCNA screened 71 genes for a dark turquoise module that were correlated with the efficacy of RTX treatment for RA (r = 0.42, P < 0.05). Through the calculation of gene significance (GS) and module membership (MM), 12 important genes were identified; in addition, 21 important genes were screened by the LASSO regression model; two key genes were obtained from the intersection between the important genes. Then, BANK1 (AUC = 0.704, P < 0.05) was identified as a potential biomarker to predict the efficacy of RTX treatment for RA by ROC curve evaluation of the treatment and validation groups. BANK1 gene expression was significantly decreased after RTX treatment, and a statistically significant difference was found (log FC = - 2.08, P < 0.05). Immune cell infiltration analysis revealed that the infiltration of CD4 + T cell memory subset was increased in the group with high BANK1 expression, and a statistically significant difference was found (P < 0.05). CONCLUSIONS BANK1 can be used as a potential biomarker to predict the response of RTX treatment in RA patients. Key Points • Identifying the hub genes BANK1 as a potential biomarker to predict the response of RTX treatment in RA patients and confirming it in validation data. • Using the WGCNA approach and LASSO analyses to identify the BANK1 in a data set consisting of two GEO data merged and assessing the correlations between BANK1 and immune infiltration by CIBERSORT algorithm.
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Affiliation(s)
- Shan Zhang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Peiting Li
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Pengjia Wu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Lei Yang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Xiaoxia Liu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Jun Liu
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Yong Zhang
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China
| | - Jiashun Zeng
- Rheumatology and Immunology Department, Affiliated Hospital of Guizhou Medical University, Yunyan District, 28 Guiyi Street, Guiyang, 550004, Guizhou, China.
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Wang J, Conlon D, Rivellese F, Nerviani A, Lewis MJ, Housley W, Levesque MC, Cao X, Cuff C, Long A, Pitzalis C, Ruzek MC. Synovial Inflammatory Pathways Characterize Anti-TNF-Responsive Rheumatoid Arthritis Patients. Arthritis Rheumatol 2022; 74:1916-1927. [PMID: 35854416 DOI: 10.1002/art.42295] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE This study was undertaken to understand the mechanistic basis of response to anti-tumor necrosis factor (anti-TNF) therapies and to determine whether transcriptomic changes in the synovium are reflected in peripheral protein markers. METHODS Synovial tissue from 46 rheumatoid arthritis (RA) patients was profiled with RNA sequencing before and 12 weeks after treatment with anti-TNF therapies. Pathway and gene signature analyses were performed on RNA expression profiles of synovial biopsies to identify mechanisms that could discriminate among patients with a good response, a moderate response, or no response, according to the American College of Rheumatology (ACR)/EULAR response criteria. Serum proteins encoded by synovial genes that were differentially expressed between ACR/EULAR response groups were measured in the same patients. RESULTS Gene signatures predicted which patients would have good responses, and pathway analysis identified elevated immune pathways, including chemokine signaling, Th1/Th2 cell differentiation, and Toll-like receptor signaling, uniquely in good responders. These inflammatory pathways were correspondingly down-modulated by anti-TNF therapy only in good responders. Based on cell signature analysis, lymphocyte, myeloid, and fibroblast cell populations were elevated in good responders relative to nonresponders, consistent with the increased inflammatory pathways. Cell signatures that decreased following anti-TNF treatment were predominately associated with lymphocytes, and fewer were associated with myeloid and fibroblast populations. Following anti-TNF treatment, and only in good responders, several peripheral inflammatory proteins decreased in a manner that was consistent with corresponding synovial gene changes. CONCLUSION Collectively, these data suggest that RA patients with robust responses to anti-TNF therapies are characterized at baseline by immune pathway activation, which decreases following anti-TNF treatment. Understanding mechanisms that define patient responsiveness to anti-TNF treatment may assist in development of predictive markers of patient response and earlier treatment options.
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Affiliation(s)
- Jing Wang
- Immunology Systems Computational Biology, Genomic Research Center, AbbVie, Cambridge, Massachusetts
| | - Donna Conlon
- Immunology Discovery, AbbVie Research Center, Worcester, Massachusetts
| | - Felice Rivellese
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alessandra Nerviani
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Myles J Lewis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William Housley
- Immunology Discovery, AbbVie Research Center, Worcester, Massachusetts
| | - Marc C Levesque
- Immunology Discovery, Cambridge Research Center, Cambridge, Massachusetts
| | - Xiaohong Cao
- Immunology Systems Computational Biology, Genomic Research Center, AbbVie, Cambridge, Massachusetts
| | - Carolyn Cuff
- Immunology Discovery, AbbVie Research Center, Worcester, Massachusetts
| | - Andrew Long
- Immunology Discovery, AbbVie Research Center, Worcester, Massachusetts
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute and Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Melanie C Ruzek
- Immunology Discovery, AbbVie Research Center, Worcester, Massachusetts
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-Omic Approaches and Treatment Response in Rheumatoid Arthritis. Pharmaceutics 2022; 14:pharmaceutics14081648. [PMID: 36015273 PMCID: PMC9412998 DOI: 10.3390/pharmaceutics14081648] [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: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is an inflammatory disorder characterized by an aberrant activation of innate and adaptive immune cells. There are different drugs used for the management of RA, including disease-modifying antirheumatic drugs (DMARDs). However, a significant percentage of RA patients do not initially respond to DMARDs. This interindividual variation in drug response is caused by a combination of environmental, genetic and epigenetic factors. In this sense, recent -omic studies have evidenced different molecular signatures involved in this lack of response. The aim of this review is to provide an updated overview of the potential role of -omic approaches, specifically genomics, epigenomics, transcriptomics, and proteomics, to identify molecular biomarkers to predict the clinical efficacy of therapies currently used in this disorder. Despite the great effort carried out in recent years, to date, there are still no validated biomarkers of response to the drugs currently used in RA. -Omic studies have evidenced significant differences in the molecular profiles associated with treatment response for the different drugs used in RA as well as for different cell types. Therefore, global and cell type-specific -omic studies analyzing response to the complete therapeutical arsenal used in RA, including less studied therapies, such as sarilumab and JAK inhibitors, are greatly needed.
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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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10
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Strand V, Zhang L, Arnaud A, Connolly-Strong E, Asgarian S, Withers JB. Improvement in clinical disease activity index when treatment selection is informed by the tumor necrosis factor-ɑ inhibitor molecular signature response classifier: analysis from the study to accelerate information of molecular signatures in rheumatoid arthritis. Expert Opin Biol Ther 2022; 22:801-807. [PMID: 35442122 DOI: 10.1080/14712598.2022.2066972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND A blood-based molecular signature response classifier (MSRC) predicts non-response to tumor necrosis factor-ɑ inhibitors (TNFi) in rheumatoid arthritis (RA). RESEARCH DESIGN AND METHODS This is an interim analysis of data collected in the Study to Accelerate Information of Molecular Signatures (AIMS) in RA from patients who received the MSRC test between September 2020 and November 2021. Absolute changes in clinical disease activity index (CDAI) scores from baseline were evaluated at 12 weeks (n = 470) and 24 weeks (n = 274). RESULTS Predicted TNFi non-responders who received a biologic or targeted synthetic disease-modifying antirheumatic drug (b/tsDMARD) with an alternative mechanism of action (altMOA) experienced up to 1.8-fold greater improvements in CDAI scores than those treated with a TNFi (12 weeks: 12.2 vs 8.0; p-value = 0.083; 24 weeks: 14.2 vs 7.8 p-value = 0.009). In patients with a molecular signature of non-response to TNFi in high disease activity at baseline, this corresponded to 43.2% relative improvement in achieving a lower CDAI disease activity level when likely TNFi non-responders were treated with a non-TNFi therapy (38.9% vs 55.7%). Commensurate improvements in efficiency of spend are expected when TNFi are avoided in favor of altMOA. CONCLUSIONS RA treatment selection informed by MSRC test results improves clinical outcomes in real-world care and offers improvements in efficiency of healthcare spending.
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Affiliation(s)
- Vibeke Strand
- Division of Immunology/Rheumatology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Lixia Zhang
- Scipher Medicine Corporation, Waltham, MA, USA
| | - Alix Arnaud
- Scipher Medicine Corporation, Waltham, MA, USA
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Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease. J Funct Biomater 2022; 13:jfb13020036. [PMID: 35466218 PMCID: PMC9036297 DOI: 10.3390/jfb13020036] [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: 03/08/2022] [Revised: 03/25/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
Neutralising monoclonal antibodies for tumour necrosis factor (TNF) has been widely used to treat Crohn’s disease (CD) in clinical practice. However, differential individual response necessitates a therapeutic response assessment of anti-TNF agents in CD patients for optimizing therapeutic strategy. We aimed to predict anti-TNF therapy response in CD patients using transcriptome analyses. Transcriptome analyses were performed using data from the Gene Expression Omnibus, GeneCards, and Human Protein Atlas databases. The significantly mitigated biological functions associated with anti-TNF therapy resistance in CD patients encompassed immune pathways, including Interleukin-17 (IL-17) signaling, cytokine-cytokine receptor interaction, and rheumatoid arthritis. The scores of immune cell markers, including neutrophils, monocytes, and macrophages/monocytes were also significantly decreased in non-responders compared with that measured in anti-TNF therapy responders. The KAT2B gene, associated with IL-17 cytokine mediated neutrophil mobilization and activation, was significantly under-expressed in both tissue and peripheral blood mononuclear cells (PBMCs) in anti-TNF therapy-resistant CD patients. The reduced expression of several pro-inflammatory cytokines due to down-regulated IL-17 signaling, is suggestive of the primary non-response to anti-TNF agents in CD patients. Furthermore, the PBMC KAT2B gene signature may be a promising pre-treatment prognostic biomarker for anti-TNF drug response in CD patients.
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A Molecular Signature Response Classifier to Predict Inadequate Response to Tumor Necrosis Factor-α Inhibitors: The NETWORK-004 Prospective Observational Study. Rheumatol Ther 2021; 8:1159-1176. [PMID: 34148193 PMCID: PMC8214458 DOI: 10.1007/s40744-021-00330-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction Timely matching of patients to beneficial targeted therapy is an unmet need in rheumatoid arthritis (RA). A molecular signature response classifier (MSRC) that predicts which patients with RA are unlikely to respond to tumor necrosis factor-α inhibitor (TNFi) therapy would have wide clinical utility. Methods The protein–protein interaction map specific to the rheumatoid arthritis pathophysiology and gene expression data in blood patient samples was used to discover a molecular signature of non-response to TNFi therapy. Inadequate response predictions were validated in blood samples from the CERTAIN cohort and a multicenter blinded prospective observational clinical study (NETWORK-004) among 391 targeted therapy-naïve and 113 TNFi-exposed patient samples. The primary endpoint evaluated the ability of the MSRC to identify patients who inadequately responded to TNFi therapy at 6 months according to ACR50. Additional endpoints evaluated the prediction of inadequate response at 3 and 6 months by ACR70, DAS28-CRP, and CDAI. Results The 23-feature molecular signature considers pathways upstream and downstream of TNFα involvement in RA pathophysiology. Predictive performance was consistent between the CERTAIN cohort and NETWORK-004 study. The NETWORK-004 study met primary and secondary endpoints. A molecular signature of non-response was detected in 45% of targeted therapy-naïve patients. The MSRC had an area under the curve (AUC) of 0.64 and patients were unlikely to adequately respond to TNFi therapy according to ACR50 at 6 months with an odds ratio of 4.1 (95% confidence interval 2.0–8.3, p value 0.0001). Odds ratios (3.4–8.8) were significant (p value < 0.01) for additional endpoints at 3 and 6 months, with AUC values up to 0.74. Among TNFi-exposed patients, the MSRC had an AUC of up to 0.83 and was associated with significant odds ratios of 3.3–26.6 by ACR, DAS28-CRP, and CDAI metrics. Conclusion The MSRC stratifies patients according to likelihood of inadequate response to TNFi therapy and provides patient-specific data to guide therapy choice in RA for targeted therapy-naïve and TNFi-exposed patients. Supplementary Information The online version contains supplementary material available at 10.1007/s40744-021-00330-y. A blood-based molecular signature response classifier (MSRC) integrating next-generation RNA sequencing data with clinical features predicts the likelihood that a patient with rheumatoid arthritis will have an inadequate response to TNFi therapy. Treatment selection guided by test results, with likely inadequate responders appropriately redirected to a different therapy, could improve response rates to TNFi therapies, generate healthcare cost savings, and increase rheumatologists’ confidence in prescribing decisions and altered treatment choices. The MSRC described in this study predicts the likelihood of inadequate response to TNFi therapies among targeted therapy-naïve and TNFi-exposed patients in a multicenter, 24-week blinded prospective clinical study: NETWORK-004. Patients with a molecular signature of non-response are less likely to have an adequate response to TNFi therapies than those patients lacking the signature according to ACR50, ACR70, CDAI, and DAS28-CRP with significant odds ratios of 3.4–8.8 for targeted therapy-naïve patients and 3.3–26.6 for TNFi-exposed patients. This MSRC provides a solution to the long-standing need for precision medicine tools to predict drug response in rheumatoid arthritis—a heterogeneous and progressive disease with an abundance of therapeutic options. These data validate the performance of the MSRC in a blinded prospective clinical study of targeted therapy-naïve and TNFi therapy-exposed patients.
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Mezghiche I, Yahia-Cherbal H, Rogge L, Bianchi E. Novel approaches to develop biomarkers predicting treatment responses to TNF-blockers. Expert Rev Clin Immunol 2021; 17:331-354. [PMID: 33622154 DOI: 10.1080/1744666x.2021.1894926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: Chronic inflammatory diseases (CIDs) cause significant morbidity and are a considerable burden for the patients in terms of pain, impaired function, and diminished quality of life. Important progress in CID treatment has been obtained with biological therapies, such as tumor-necrosis-factor blockers. However, more than a third of the patients fail to respond to these inhibitors and are exposed to the side effects of treatment, without the benefits. Therefore, there is a strong interest in developing tools to predict response of patients to biologics. Areas covered: The authors searched PubMed for recent studies on biomarkers for disease assessment and prediction of therapeutic responses, focusing on the effect of TNF blockers on immune responses in spondyloarthritis (SpA), and other CID, in particular rheumatoid arthritis and inflammatory bowel disease. Conclusions will be drawn about the possible development of predictive biomarkers for response to treatment. Expert opinion: No validated biomarker is currently available to predict treatment response in CID. New insight could be generated through the development of new bioinformatic modeling approaches to combine multidimensional biomarkers that explain the different genetic, immunological and environmental determinants of therapeutic responses.
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Affiliation(s)
- Ikram Mezghiche
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Université De Paris, Sorbonne Paris Cité, Paris, France
| | - Hanane Yahia-Cherbal
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Fondation AP-HP, Paris, France
| | - Lars Rogge
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Elisabetta Bianchi
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
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Tao W, Concepcion AN, Vianen M, Marijnissen ACA, Lafeber FPGJ, Radstake TRDJ, Pandit A. Multiomics and Machine Learning Accurately Predict Clinical Response to Adalimumab and Etanercept Therapy in Patients With Rheumatoid Arthritis. Arthritis Rheumatol 2021; 73:212-222. [PMID: 32909363 PMCID: PMC7898388 DOI: 10.1002/art.41516] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To predict response to anti-tumor necrosis factor (anti-TNF) prior to treatment in patients with rheumatoid arthritis (RA), and to comprehensively understand the mechanism of how different RA patients respond differently to anti-TNF treatment. METHODS Gene expression and/or DNA methylation profiling on peripheral blood mononuclear cells (PBMCs), monocytes, and CD4+ T cells obtained from 80 RA patients before they began either adalimumab (ADA) or etanercept (ETN) therapy was studied. After 6 months, treatment response was evaluated according to the European League Against Rheumatism criteria for disease response. Differential expression and methylation analyses were performed to identify the response-associated transcription and epigenetic signatures. Using these signatures, machine learning models were built by random forest algorithm to predict response prior to anti-TNF treatment, and were further validated by a follow-up study. RESULTS Transcription signatures in ADA and ETN responders were divergent in PBMCs, and this phenomenon was reproduced in monocytes and CD4+ T cells. The genes up-regulated in CD4+ T cells from ADA responders were enriched in the TNF signaling pathway, while very few pathways were differential in monocytes. Differentially methylated positions (DMPs) were strongly hypermethylated in responders to ETN but not to ADA. The machine learning models for the prediction of response to ADA and ETN using differential genes reached an overall accuracy of 85.9% and 79%, respectively. The models using DMPs reached an overall accuracy of 84.7% and 88% for ADA and ETN, respectively. A follow-up study validated the high performance of these models. CONCLUSION Our findings indicate that machine learning models based on molecular signatures accurately predict response before ADA and ETN treatment, paving the path toward personalized anti-TNF treatment.
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Affiliation(s)
- Weiyang Tao
- University Medical Center Utrecht and Utrecht UniversityThe Netherlands
| | | | - Marieke Vianen
- University Medical Center Utrecht and Utrecht UniversityThe Netherlands
| | | | | | | | - Aridaman Pandit
- University Medical Center Utrecht and Utrecht UniversityThe Netherlands
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15
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Whole Transcription Profile of Responders to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease. Pharmaceutics 2021; 13:pharmaceutics13010077. [PMID: 33429950 PMCID: PMC7830359 DOI: 10.3390/pharmaceutics13010077] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Up to 30% of patients with pediatric inflammatory bowel disease (IBD) do not respond to anti-Tumor Necrosis Factor (anti-TNF) therapy. The aim of this study was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD. Methods: An observational, longitudinal, prospective cohort study was conducted. The study population comprised 38 patients with IBD aged < 18 years who started treatment with infliximab or adalimumab (29 responders and nine non-responders). Whole gene expression profiles from total RNA isolated from whole blood samples of six responders and six non-responders taken before administration of the biologic and after two weeks of therapy were analyzed using next-generation RNA sequencing. The expression of six selected genes was measured for purposes of validation in all of the 38 patients recruited using qPCR. Results: Genes were differentially expressed in non-responders and responders (32 before initiation of treatment and 44 after two weeks, Log2FC (Fold change) >0.6 or <−0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B, and GBP1 were overexpressed in non-responders two weeks after initiation of anti-TNF treatment (Log2FC 1.05, 1.21, and 1.08, respectively, p value < 0.05). Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.
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16
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Gene Signatures of Early Response to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease. Int J Mol Sci 2020; 21:ijms21093364. [PMID: 32397546 PMCID: PMC7247673 DOI: 10.3390/ijms21093364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 02/06/2023] Open
Abstract
Around a 20–30% of inflammatory bowel disease (IBD) patients are diagnosed before they are 18 years old. Anti-TNF drugs can induce and maintain remission in IBD, however, up to 30% of patients do not respond. The aim of the work was to identify markers that would predict an early response to anti-TNF drugs in pediatric patients with IBD. The study population included 43 patients aged <18 years with IBD who started treatment with infliximab or adalimumab. Patients were classified into primary responders (n = 27) and non-responders to anti-TNF therapy (n = 6). Response to treatment could not be analyzed in 10 patients. Response was defined as a decrease in over 15 points in the disease activity indexes from week 0 to week 10 of infliximab treatment or from week 0 to week 26 of adalimumab treatment. The expression profiles of nine genes in total RNA isolated from the whole-blood of pediatric IBD patients taken before biologic administration and after 2 weeks were analyzed using qPCR and the 2−∆∆Ct method. Before initiation and after 2 weeks of treatment the expression of SMAD7 was decreased in patients who were considered as non-responders (p value < 0.05). Changes in expression were also observed for TLR2 at T0 and T2, although that did not reach the level of statistical significance. In addition, the expression of DEFA5 decreased 1.75-fold during the first 2 weeks of anti-TNF treatment in responders, whereas no changes were observed in non-responders. Expression of the SMAD7 gene is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD. TLR2 and DEFA5 need to be validated in larger studies.
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Bulk and single cell transcriptomic data indicate that a dichotomy between inflammatory pathways in peripheral blood and arthritic joints complicates biomarker discovery. Cytokine 2020; 127:154960. [DOI: 10.1016/j.cyto.2019.154960] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/03/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022]
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Molecular profiling of rheumatoid arthritis patients reveals an association between innate and adaptive cell populations and response to anti-tumor necrosis factor. Arthritis Res Ther 2019; 21:216. [PMID: 31647025 PMCID: PMC6813112 DOI: 10.1186/s13075-019-1999-3] [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] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022] Open
Abstract
Background The goal of this study is to use comprehensive molecular profiling to characterize clinical response to anti-TNF therapy in a real-world setting and identify reproducible markers differentiating good responders and non-responders in rheumatoid arthritis (RA). Methods Whole-blood mRNA, plasma proteins, and glycopeptides were measured in two cohorts of biologic-naïve RA patients (n = 40 and n = 36) from the Corrona CERTAIN (Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory coNditions) registry at baseline and after 3 months of anti-TNF treatment. Response to treatment was categorized by EULAR criteria. A cell type-specific data analysis was conducted to evaluate the involvement of the most common immune cell sub-populations. Findings concordant between the two cohorts were further assessed for reproducibility using selected NCBI-GEO datasets and clinical laboratory measurements available in the CERTAIN database. Results A treatment-related signature suggesting a reduction in neutrophils, independent of the status of response, was indicated by a high level of correlation (ρ = 0.62; p < 0.01) between the two cohorts. A baseline, response signature of increased innate cell types in responders compared to increased adaptive cell types in non-responders was identified in both cohorts. This result was further assessed by applying the cell type-specific analysis to five other publicly available RA datasets. Evaluation of the neutrophil-to-lymphocyte ratio at baseline in the remaining patients (n = 1962) from the CERTAIN database confirmed the observation (odds ratio of good/moderate response = 1.20 [95% CI = 1.03–1.41, p = 0.02]). Conclusion Differences in innate/adaptive immune cell type composition at baseline may be a major contributor to response to anti-TNF treatment within the first 3 months of therapy.
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Aterido A, Cañete JD, Tornero J, Blanco F, Fernández-Gutierrez B, Pérez C, Alperi-López M, Olivè A, Corominas H, Martínez-Taboada V, González I, Fernández-Nebro A, Erra A, López-Lasanta M, López Corbeto M, Palau N, Marsal S, Julià A. A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. Front Immunol 2019; 10:1459. [PMID: 31312201 PMCID: PMC6614444 DOI: 10.3389/fimmu.2019.01459] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Rheumatoid arthritis (RA) is the most frequent autoimmune disease involving the joints. Although anti-TNF therapies have proven effective in the management of RA, approximately one third of patients do not show a significant clinical response. The objective of this study was to identify new genetic variation associated with the clinical response to anti-TNF therapy in RA. Methods: We performed a sequential multi-omic analysis integrating different sources of molecular information. First, we extracted the RNA from synovial biopsies of 11 RA patients starting anti-TNF therapy to identify gene coexpression modules (GCMs) in the RA synovium. Second, we analyzed the transcriptomic association between each GCM and the clinical response to anti-TNF therapy. The clinical response was determined at week 14 using the EULAR criteria. Third, we analyzed the association between the GCMs and anti-TNF response at the genetic level. For this objective, we used genome-wide data from a cohort of 348 anti-TNF treated patients from Spain. The GCMs that were significantly associated with the anti-TNF response were then tested for validation in an independent cohort of 2,706 anti-TNF treated patients. Finally, the functional implication of the validated GCMs was evaluated via pathway and cell type epigenetic enrichment analyses. Results: A total of 149 GCMs were identified in the RA synovium. From these, 13 GCMs were found to be significantly associated with anti-TNF response (P < 0.05). At the genetic level, we detected two of the 13 GCMs to be significantly associated with the response to adalimumab (P = 0.0015) and infliximab (P = 0.021) in the Spain cohort. Using the independent cohort of RA patients, we replicated the association of the GCM associated with the response to adalimumab (P = 0.0019). The validated module was found to be significantly enriched for genes involved in the nucleotide metabolism (P = 2.41e-5) and epigenetic marks from immune cells, including CD4+ regulatory T cells (P = 0.041). Conclusions: These findings show the existence of a drug-specific genetic basis for anti-TNF response, thereby supporting treatment stratification in the search for response biomarkers in RA.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juan D Cañete
- Rheumatology Department, Hospital Clínic de Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jesús Tornero
- Rheumatology Department, Hospital Universitario De Guadalajara, Guadalajara, Spain
| | - Francisco Blanco
- Rheumatology Department, INIBIC-Hospital Universitario A Coruña, A Coruña, Spain
| | | | - Carolina Pérez
- Rheumatology Department, Parc de Salut Mar, Barcelona, Spain
| | | | - Alex Olivè
- Rheumatology Department, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Héctor Corominas
- Rheumatology Department, Hospital Moisès Broggi, Barcelona, Spain
| | | | - Isidoro González
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | - Antonio Fernández-Nebro
- UGC Reumatología, Instituto Investigación Biomédica Málaga, Hospital Regional Universitario, Universidad de Málaga, Málaga, Spain
| | - Alba Erra
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
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20
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Utilizing a PTPN22 gene signature to predict response to targeted therapies in rheumatoid arthritis. J Autoimmun 2019; 101:121-130. [PMID: 31030958 DOI: 10.1016/j.jaut.2019.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/26/2022]
Abstract
Despite the development of several targeted therapies for rheumatoid arthritis (RA), there is still no reliable drug-specific predictor to assist rheumatologists in selecting the most effective targeted therapy for each patient. Recently, a gene signature caused by impaired induction of PTPN22 in anti-CD3 stimulated peripheral blood mononuclear cells (PBMC) was observed in healthy at-risk individuals. However, the downstream target genes of PTPN22 and the molecular mechanisms regulating its expression are still poorly understood. Here we report that the PTPN22 gene signature is also present in PBMC from patients with active RA and can be reversed after effective treatment. The expression of PTPN22 correlates with that of more than 1000 genes in Th cells of anti-CD3 stimulated PBMC of healthy donors and is inhibited by TNFα or CD28 signals, but not IL-6, through distinct mechanisms. In addition, the impaired induction of PTPN22 in PBMC of patients with active RA can be normalized in vitro by several targeted therapies. More importantly, the in vitro normalization of PTPN22 expression correlates with clinical response to the targeted therapies in a longitudinal RA cohort. Thus, in vitro normalization of PTPN22 expression by targeted therapies can potentially be used to predict clinical response.
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21
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Lequerré T, Rottenberg P, Derambure C, Cosette P, Vittecoq O. Predictors of treatment response in rheumatoid arthritis. Joint Bone Spine 2019; 86:151-158. [DOI: 10.1016/j.jbspin.2018.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2018] [Indexed: 12/13/2022]
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22
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Paran D, Smith Y, Pundak S, Arad U, Levartovsky D, Kaufman I, Wollman J, Furer V, Broyde A, Elalouf O, Caspi D, Pel S, Elkayam O. Expression levels of selected genes can predict individual rheumatoid arthritis patient response to tumor necrosis factor alpha blocker treatment. Curr Med Res Opin 2018; 34:1777-1783. [PMID: 29569514 DOI: 10.1080/03007995.2018.1443581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVES Rheumatoid arthritis (RA) patients have many therapeutic options; however, tools to predict individual patient response are limited. The Genefron personal diagnostic kit, developed by analyzing large datasets, utilizes selected interferon stimulated gene expressions to predict treatment response. This study evaluates the kit's prediction accuracy of individual RA patients' response to tumor necrosis alpha (TNFα) blockers. METHODS A retrospective analysis was performed on RA patients reported in published datasets. A prospective analysis assessed RA patients, before and 3 months after starting a TNFα blocker. Clinical response was evaluated according to EULAR response criteria. Blood samples were obtained before starting treatment and were analyzed utilizing the kit which measures expression levels of selected genes by quantitative real time polymerase chain reaction (PCR). ROC analysis was applied to the published datasets and the prospective data. RESULTS The Genefron kit analysis of retrospective data predicted the response to a TNFα blocker in 53 of 61 RA patients (86.8% accuracy). In the prospective analysis, the kit predicted the response in 16 of 18 patients (89% accuracy) achieving a EULAR moderate response, and in 15 of 18 patients achieving a EULAR good response (83.3% accuracy). ROC analysis applied to the two published datasets yielded an AUC of 0.89. ROC analysis applied to the prospective data yielded an AUC of 0.83 (sensitivity - 100%, specificity - 75%) The statistical power obtained in the prospective study was .9. CONCLUSION The diagnostic kit predicted the response to TNFα blockers in a high percentage of patients assessed retrospectively or prospectively. This personal kit may guide selection of a suitable biological drug for the individual RA patient.
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Affiliation(s)
- Daphna Paran
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Yoav Smith
- b Genomic Data Analysis Hadassah Medical School Hebrew University , Jerusalem , Israel
| | | | - Uri Arad
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - David Levartovsky
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Ilana Kaufman
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Jonathan Wollman
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Victoria Furer
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Adi Broyde
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Ofir Elalouf
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Dan Caspi
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Sara Pel
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
| | - Ori Elkayam
- a Rheumatology Department, Tel-Aviv Medical Center and the Sackler School of Medicine , Tel-Aviv University , Israel
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Cuppen BVJ, Rossato M, Fritsch-Stork RDE, Concepcion AN, Linn-Rasker SP, Bijlsma JWJ, van Laar JM, Lafeber FPJG, Radstake TR. RNA sequencing to predict response to TNF-α inhibitors reveals possible mechanism for nonresponse in smokers. Expert Rev Clin Immunol 2018; 14:623-633. [PMID: 29808722 DOI: 10.1080/1744666x.2018.1480937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice. METHODS The eighty most extreme responders and nonresponders to TNFi therapy were selected from the observational BiOCURA cohort. RNA sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and nonresponders was investigated. Promising targets were technically replicated and validated in n = 40 new patients using qPCR assays. RESULTS Before therapy initiation, nonresponders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (p = 0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (p < 0.0001). CONCLUSIONS The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.
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Affiliation(s)
- Bart V J Cuppen
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Marzia Rossato
- b Laboratory of Translational Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,c Department of Biotechnology , University of Verona , Verona , Italy
| | - Ruth D E Fritsch-Stork
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,d 1st Medical Department & Ludwig Boltzmann Institute of Osteology at the Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling , Hanusch Hospital , Vienna , Austria.,e Sigmund Freud University , Vienna , Austria
| | - Arno N Concepcion
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | | | - Johannes W J Bijlsma
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Jacob M van Laar
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Floris P J G Lafeber
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - Timothy R Radstake
- a Rheumatology & Clinical Immunology , University Medical Center Utrecht , Utrecht , The Netherlands.,b Laboratory of Translational Immunology , University Medical Center Utrecht , Utrecht , The Netherlands
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A novel gene and pathway-level subtyping analysis scheme to understand biological mechanisms in complex disease: a case study in rheumatoid arthritis. Genomics 2018; 111:375-382. [PMID: 29481842 DOI: 10.1016/j.ygeno.2018.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 02/14/2018] [Accepted: 02/20/2018] [Indexed: 11/20/2022]
Abstract
Complex diseases have heterogeneous underlying molecular mechanisms. In order to improve the diagnosis and treatment of disease, it is vital to stratify patients into homogeneous subgroups that share a similar disease etiology. In this study, we performed gene-level subtyping analysis on two independent Rheumatoid Arthritis gene expression cohorts from different ethnic groups to discover the possible disease mechanisms associated with each subtype. Also, a novel pathway-level analysis is proposed to increase the subtyping robustness and facilitate biological interpretation. This approach could stratify RA patients into two robust and homogeneous groups with differing activation of central signal transduction pathways and pro-inflammatory cytokines in the pathogenesis of RA. Such a methodology can help understand disease mechanisms at play in different patient sub-populations and also potentially explain why some patients don't respond to anti-TNF treatment.
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Theory of signs and statistical approach to big data in assessing the relevance of clinical biomarkers of inflammation and oxidative stress. Proc Natl Acad Sci U S A 2018; 115:2473-2477. [PMID: 29463702 DOI: 10.1073/pnas.1719807115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Biomarkers are widely used not only as prognostic or diagnostic indicators, or as surrogate markers of disease in clinical trials, but also to formulate theories of pathogenesis. We identify two problems in the use of biomarkers in mechanistic studies. The first problem arises in the case of multifactorial diseases, where different combinations of multiple causes result in patient heterogeneity. The second problem arises when a pathogenic mediator is difficult to measure. This is the case of the oxidative stress (OS) theory of disease, where the causal components are reactive oxygen species (ROS) that have very short half-lives. In this case, it is usual to measure the traces left by the reaction of ROS with biological molecules, rather than the ROS themselves. Borrowing from the philosophical theories of signs, we look at the different facets of biomarkers and discuss their different value and meaning in multifactorial diseases and system medicine to inform their use in patient stratification in personalized medicine.
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Derambure C, Dzangue-Tchoupou G, Berard C, Vergne N, Hiron M, D'Agostino MA, Musette P, Vittecoq O, Lequerré T. Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis. Arthritis Res Ther 2017; 19:109. [PMID: 28545499 PMCID: PMC5445375 DOI: 10.1186/s13075-017-1319-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/05/2017] [Indexed: 11/10/2022] Open
Abstract
Background In the current context of personalized medicine, one of the major challenges in the management of rheumatoid arthritis (RA) is to identify biomarkers that predict drug responsiveness. From the European APPRAISE trial, our main objective was to identify a gene expression profile associated with responsiveness to abatacept (ABA) + methotrexate (MTX) and to understand the involvement of this signature in the pathophysiology of RA. Methods Whole human genome microarrays (4 × 44 K) were performed from a first subset of 36 patients with RA. Data validation by quantitative reverse-transcription (qRT)-PCR was performed from a second independent subset of 32 patients with RA. Gene Ontology and WikiPathways database allowed us to highlight the specific biological mechanisms involved in predicting response to ABA/MTX. Results From the first subset of 36 patients with RA, a combination including 87 transcripts allowed almost perfect separation between responders and non-responders to ABA/MTX. Next, the second subset of patients 32 with RA allowed validation by qRT-PCR of a minimal signature with only four genes. This latter signature categorized 81% of patients with RA with 75% sensitivity, 85% specificity and 85% negative predictive value. This combination showed a significant enrichment of genes involved in electron transport chain (ETC) pathways. Seven transcripts from ETC pathways (NDUFA6, NDUFA4, UQCRQ, ATP5J, COX7A2, COX7B, COX6A1) were significantly downregulated in responders versus non-responders to ABA/MTX. Moreover, dysregulation of these genes was independent of inflammation and was specific to ABA response. Conclusion Pre-silencing of ETC genes is associated with future response to ABA/MTX and might be a crucial key to susceptibility to ABA response. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1319-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C Derambure
- Normandie Univ, UNIROUEN, Inserm U 1245, F 76000, Rouen, France
| | | | - C Berard
- LITIS EA 4108, Computer science, information processing and systems laboratory, Normandy University, Institute for Research and Innovation in Biomedicine, 76451, Mont-Saint-Aignan, France
| | - N Vergne
- LMRS UMR 6085 CNRS, Raphaël Salem laboratory, Normandy University, 76575, Saint Étienne du Rouvray, France
| | - M Hiron
- Normandie Univ, UNIROUEN, Inserm U 905, F 76000, Rouen, France
| | - M A D'Agostino
- Departement of Rheumatology, AP-HP Ambroise Paré Hospital, University of Versailles Saint Quentin en Yvelines, 92100, Boulogne-Billancourt, France
| | - P Musette
- Normandie Univ, UNIROUEN, Inserm U 1234, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France
| | - O Vittecoq
- Normandie Univ, UNIROUEN, Inserm U 1234, Inserm CIC-CRB 1404, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France
| | - T Lequerré
- Normandie Univ, UNIROUEN, Inserm U 1234, Inserm CIC-CRB 1404, Rouen University Hospital, Department of Dermatology, F 76000, Rouen, France.
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Huang QL, Zhou FJ, Wu CB, Xu C, Qian WY, Fan DP, Cai XS. Circulating Biomarkers for Predicting Infliximab Response in Rheumatoid Arthritis: A Systematic Bioinformatics Analysis. Med Sci Monit 2017; 23:1849-1855. [PMID: 28413214 PMCID: PMC5404751 DOI: 10.12659/msm.900897] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background Infliximab shows good efficacy in treating refractory rheumatoid arthritis (RA). However, many patients responded poorly and related studies were inconsistent in predictive biomarkers. This study aimed to identify circulating biomarkers for predicting infliximab response in RA. Material/Methods Public databases of Gene Expression Omnibus (GEO) and ArrayExpress were searched for related microarray datasets, focused on the response to infliximab in RA. All peripheral blood samples were collected before infliximab treatment and gene expression profiles were measured using microarray. Differential genes associated with infliximab efficacy were analyzed. The genes recognized by half of the datasets were regarded as candidate biomarkers and validated by prospective datasets. Results Eight microarray datasets were identified with 374 blood samples of RA patients, among which 191 (51.1%) were diagnosed as non-responders in the subsequent infliximab treatment. Five genes (FKBP1A, FGF12, ANO1, LRRC31, and AKR1D1) were associated with the efficacy and recognized by half of the datasets. The 5-gene model showed a good predictive power in random- and prospective-designed studies, with AUC (area under receiver operating characteristic [ROC] curve)=0.963 and 1.000, and it was also applicable at the early phase of treatment (at week 2) for predicting the response at week 14 (AUC=1.000). In the placebo group, the model failed to predict the response (AUC=0.697), indicating the model’s specificity in infliximab treatment. Conclusions The model of FKBP1A, FGF12, ANO1, LRRC31, and AKR1D1 in peripheral blood is useful for efficiently predicting the response to infliximab treatment in rheumatoid arthritis.
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Affiliation(s)
- Qiu-Lan Huang
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Fu-Jiang Zhou
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Cheng-Bin Wu
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Chao Xu
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Wen-Ying Qian
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - De-Ping Fan
- Department of Clinical Laboratory Medicine, Jiading Lanxiang Hospital, Shanghai, China (mainland)
| | - Xu-Shan Cai
- Department of Clinical Laboratory Medicine, Maternal and Child Healthcare Hospital of Jiading, Shanghai, China (mainland)
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Davis LS, Reimold AM. Transcriptional profiling of leukocytes from rheumatoid arthritis patients before and after anti-tumor necrosis factor therapy: A comparison of anti-nuclear antibody positive and negative subsets. Exp Ther Med 2017; 13:2183-2192. [PMID: 28565826 PMCID: PMC5443193 DOI: 10.3892/etm.2017.4265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Anti-nuclear antibodies (ANAs) may be induced in patients with rheumatoid arthritis (RA) receiving anti-tumor necrosis factor (TNF) therapy with TNF inhibitors (TNFi), etanercept, infliximab or adalimumab. In the present study, 11 patients who were TNFi drug naive were started on TNFi at a time of high disease activity. Of these, all cases were positive for rheumatoid factor and 9 cases tested were positive for anti-citrullinated peptide (anti-CCP) antibodies prior to TNFi treatment. Peripheral blood mononuclear cells (PBMCs) and serum were collected from all patients before and after TNFi therapy. Serum was assayed for ANAs over time. Total cellular RNA was extracted from PBMCs and assessed using Illumina arrays. Gene expression profiles were examined for alterations in key effector pathways. After 3 or more months on TNFi, 6 patients converted to ANA-positivity. Analysis of transcripts from patients with RA who converted to ANA-positivity after 3 months on TNFi identified complex gene expression profiles that reflected a reduction in cell adhesion, cell stress and lipid metabolism transcripts. In summary, unique transcriptional profiles in PBMCs from patients with RA were observed after TNFi therapy. This pilot study suggests that transcriptional profiling is a precise method of measuring the impact of TNFi therapies and reveals novel pathways that likely influence the immune response.
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Affiliation(s)
- Laurie S Davis
- Rheumatic Diseases Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8884, USA
| | - Andreas M Reimold
- Rheumatic Diseases Division, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-8884, USA.,Rheumatology Section, Dallas VA Medical Center, Dallas, TX 75216, USA
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Stuhlmüller B, Mans K, Tandon N, Bonin MO, Smiljanovic B, Sörensen TA, Schendel P, Martus P, Listing J, Detert J, Backhaus M, Neumann T, Winchester RJ, Burmester GR, Häupl T. Genomic stratification by expression of HLA-DRB4 alleles identifies differential innate and adaptive immune transcriptional patterns - A strategy to detect predictors of methotrexate response in early rheumatoid arthritis. Clin Immunol 2016; 171:50-61. [PMID: 27570220 DOI: 10.1016/j.clim.2016.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022]
Abstract
Effective drug selection is the current challenge in rheumatoid arthritis (RA). Treatment failure may follow different pathomechanisms and therefore require investigation of molecularly defined subgroups. In this exploratory study, whole blood transcriptomes of 68 treatment-naïve early RA patients were analyzed before initiating MTX. Subgroups were defined by serologic and genetic markers. Response related signatures were interpreted using reference transcriptomes of various cell types, cytokine stimulated conditions and bone marrow precursors. HLA-DRB4-negative patients exhibited most distinctive transcriptional differences. Preponderance of transcripts associated with phagocytes and bone marrow activation indicated response and transcripts of T- and B-lymphocytes non-response. HLA-DRB4-positive patients were more heterogeneous, but also linked failure to increased adaptive immune response. RT-qPCR confirmed reliable candidate selection and independent samples of responders and non-responders the functional patterning. In summary, genomic stratification identified different molecular pathomechanisms in early RA and preponderance of innate but not adaptive immune activation suggested response to MTX therapy.
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Affiliation(s)
- Bruno Stuhlmüller
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany.
| | - Karsten Mans
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Neeraj Tandon
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Marc O Bonin
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Biljana Smiljanovic
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Till A Sörensen
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Pascal Schendel
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Peter Martus
- Institute of Clinical Epidemiology and Applied Biostatistics, University of Tübingen, Germany
| | | | - Jacqueline Detert
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Marina Backhaus
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Thomas Neumann
- Department of Rheumatology, University Medicine Jena, Germany
| | | | - Gerd-R Burmester
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
| | - Thomas Häupl
- Department of Rheumatology and Clinical Immunology, Charité University Medicine, Berlin, Germany
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Folkersen L, Brynedal B, Diaz-Gallo LM, Ramsköld D, Shchetynsky K, Westerlind H, Sundström Y, Schepis D, Hensvold A, Vivar N, Eloranta ML, Rönnblom L, Brunak S, Malmström V, Catrina A, Moerch UG, Klareskog L, Padyukov L, Berg L. Integration of known DNA, RNA and protein biomarkers provides prediction of anti-TNF response in rheumatoid arthritis: results from the COMBINE study. Mol Med 2016; 22:322-328. [PMID: 27532898 DOI: 10.2119/molmed.2016.00078] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/24/2016] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE In rheumatoid arthritis (RA) several recent efforts have sought to discover means of predicting which patients would benefit from treatment. However, results have been discrepant with few successful replications. Our objective was to build a biobank with DNA, RNA and protein measurements to test the claim that the current state-of-the-art precision medicine will benefit RA patients. METHODS We collected 451 blood samples from 61 healthy individuals and 185 RA patients initiating treatment, before treatment initiation and at a 3 month follow-up time. All samples were subjected to high-throughput RNA sequencing, DNA genotyping, extensive proteomics and flow cytometry measurements, as well as comprehensive clinical phenotyping. Literature review identified 2 proteins, 52 single-nucleotide polymorphisms (SNPs) and 72 gene-expression biomarkers that had previously been proposed as predictors of TNF inhibitor response (∆DAS28-CRP). RESULTS From these published TNFi biomarkers we found that 2 protein, 2 SNP and 8 mRNA biomarkers could be replicated in the 59 TNF initiating patients. Combining these replicated biomarkers into a single signature we found that we could explain 51% of the variation in ∆DAS28-CRP. This corresponds to a sensitivity of 0.73 and specificity of 0.78 for the prediction of three month ∆DAS28-CRP better than -1.2. CONCLUSIONS The COMBINE biobank is currently the largest collection of multi-omics data from RA patients with high potential for discovery and replication. Taking advantage of this we surveyed the current state-of-the-art of drug-response stratification in RA, and identified a small set of previously published biomarkers available in peripheral blood which predicts clinical response to TNF blockade in this independent cohort.
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Affiliation(s)
- Lasse Folkersen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Boel Brynedal
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lina Marcela Diaz-Gallo
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Ramsköld
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Klementy Shchetynsky
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Helga Westerlind
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yvonne Sundström
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Danika Schepis
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Aase Hensvold
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Nancy Vivar
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | - Lars Rönnblom
- Department of Medical Sciences, Uppsala Universitet, Uppsala, Sweden
| | - Søren Brunak
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Vivianne Malmström
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anca Catrina
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | - Lars Klareskog
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Louise Berg
- Unit of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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Miyoshi F, Honne K, Minota S, Okada M, Ogawa N, Mimura T. A novel method predicting clinical response using only background clinical data in RA patients before treatment with infliximab. Mod Rheumatol 2016; 26:813-816. [PMID: 27146242 DOI: 10.3109/14397595.2016.1168536] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The aim of the present study was to generate a novel method for predicting the clinical response to infliximab (IFX), using a machine-learning algorithm with only clinical data obtained before the treatment in rheumatoid arthritis (RA) patients. METHODS We obtained 32 variables out of the clinical data on the patients from two independent hospitals. Next, we selected both clinical parameters and machine-learning algorithms and decided the candidates of prediction method. These candidates were verified by clinical variables on different patients from two other hospitals. Finally, we decided the prediction method to achieve the highest score. RESULTS The combination of multilayer perceptron algorithm (neural network) and nine clinical parameters shows the best accuracy performance. This method could predict the good or moderate response to IFX with 92% accuracy. The sensitivity of this method was 96.7%, while the specificity was 75%. CONCLUSIONS We have developed a novel method for predicting the clinical response using only background clinical data in RA patients before treatment with IFX. Our method for predicting the response to IFX in RA patients may have advantages over the other previous methods in several points including easy usability, cost-effectiveness and accuracy.
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Affiliation(s)
- Fumihiko Miyoshi
- a Department of Rheumatology and Applied Immunology, Faculty of Medicine , Saitama Medical University , Saitama , Japan
| | - Kyoko Honne
- b Division of Rheumatology and Clinical Immunology , Jichi Medical University , Tochigi , Japan
| | - Seiji Minota
- b Division of Rheumatology and Clinical Immunology , Jichi Medical University , Tochigi , Japan
| | - Masato Okada
- c Immuno-Rheumatology Center, St. Luke's International Hospital , Tokyo , Japan , and
| | - Noriyoshi Ogawa
- d Division of Immunology and Rheumatology , Internal Medicine 3, Hamamatsu University School of Medicine , Hamamatsu , Japan
| | - Toshihide Mimura
- a Department of Rheumatology and Applied Immunology, Faculty of Medicine , Saitama Medical University , Saitama , Japan
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Filkova M, Cope A, Mant T, Galloway J. Is there a role of synovial biopsy in drug development? BMC Musculoskelet Disord 2016; 17:172. [PMID: 27094362 PMCID: PMC4837502 DOI: 10.1186/s12891-016-1028-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/09/2016] [Indexed: 12/27/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease which causes significant pain, joint deformity, functional disability. The pathological hallmark of RA is inflammation of the synovium characterized by involvement of inflammatory and resident stromal cells, soluble mediators and signalling pathways leading to irreversible joint destruction. The treatment goal in RA has evolved over the last decade towards a target of disease remission that is achieved in less than a third of patients in clinical trials. The lack of therapeutic response to current treatments is suggestive of alternative drivers of RA pathogenesis that might serve as promising therapeutic targets. There are data to justify the use of synovial tissue in early drug development. Synovial tissue represents an appropriate compartment to be studied in patients with inflammatory arthritis and provides information that is distinct from peripheral blood. Modern techniques have made the procedure much more accessible and ultrasound guided biopsies represent a safe and acceptable option. Advances in analytic technologies allowing transcriptomic level of analysis can provide unique inside to target organ/tissue following the exposure to investigational medicinal product. However, there are still caveats with regard to both the choice of technique and analytical methods. Therefore the significance of synovial biopsy remains to be determined in future clinical trials. The aim of the current debate is to explore the potential for accessing and evaluating synovial tissue in early drug development, to summarize lessons we have learned from clinical trials and to discuss the challenges that have arisen so far.
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Affiliation(s)
- Maria Filkova
- Academic Department of Rheumatology, Weston Education Centre, King's College London, Cutcombe Road, SE5 9RJ, London, UK
| | - Andrew Cope
- Academic Department of Rheumatology, Weston Education Centre, King's College London, Cutcombe Road, SE5 9RJ, London, UK
| | - Tim Mant
- Quintiles Drug Research Unit at Guy's Hospital, London, UK
| | - James Galloway
- Academic Department of Rheumatology, Weston Education Centre, King's College London, Cutcombe Road, SE5 9RJ, London, UK.
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Márquez A, Martín J, Carmona FD. Emerging aspects of molecular biomarkers for diagnosis, prognosis and treatment response in rheumatoid arthritis. Expert Rev Mol Diagn 2016; 16:663-75. [DOI: 10.1080/14737159.2016.1174579] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Smith SL, Eyre S, Yarwood A, Hyrich K, Morgan AW, Wilson AG, Isaacs J, Plant D, Barton A. Investigating CD11c expression as a potential genomic biomarker of response to TNF inhibitor biologics in whole blood rheumatoid arthritis samples. Arthritis Res Ther 2015; 17:359. [PMID: 26667261 PMCID: PMC4704535 DOI: 10.1186/s13075-015-0868-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/20/2015] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Gene expression profiling is rapidly becoming a useful and informative tool in a much needed area of research. Identifying patients as to whether they will respond or not to a given treatment before prescription is not only essential to optimise treatment outcome but also to lessen the economic burden that such drugs can have on healthcare resources. In rheumatoid arthritis (RA), there is of yet no genetic/genomic biomarker which can accurately predict response to TNF inhibitor biologics prior to treatment, despite much interest in this area. Multiple studies have reported findings on potential candidate genes; however, due to relatively small sample sizes or lack of sufficient validation, results have been disappointingly inconsistent. The aim of this research was to further explore the predictive value of a previously reported association between CD11c expression and response to the TNF inhibitor biologics, adalimumab and etanercept. METHODS Real-time qPCR was performed using whole blood RNA samples obtained from seventy-five rheumatoid arthritis patients about to commence treatment with a TNF inhibitor biologic drug, whose response status was determined at 3-month follow-up using the EULAR classification criteria. Relative quantification of CD11c using the comparative CT method outputted differential expression between good-responders and non-responders as a fold-change. RESULTS Relative expression of CD11c in patients receiving TNF inhibitor biologics yielded a decrease of 1.025 fold in good-responders as compared to non-responders (p-value = 0.36). Upon stratification of patients dependent upon the specific drug administered, adalimumab or etanercept, similar findings to the full cohort were observed, decreases of 1.015 (p-value = 0.33) and 1.032 fold (p-value = 0.13) in good-responders compared to non-responders, respectively. CONCLUSION The results from this study reveal that CD11c expression does not correlate with response to TNF inhibitor biologics when tested for within pre-treatment whole blood samples of rheumatoid arthritis patients.
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Affiliation(s)
- Samantha Louise Smith
- Arthritis Research UK, Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, the University of Manchester, Manchester, UK.
| | - Stephen Eyre
- Arthritis Research UK, Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, the University of Manchester, Manchester, UK.
| | - Annie Yarwood
- Arthritis Research UK, Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, the University of Manchester, Manchester, UK.
| | - Kimme Hyrich
- Arthritis Research UK, Centre for Epidemiology, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK.
| | - Ann W Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds and NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - A G Wilson
- UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Dublin, Ireland.
| | - John Isaacs
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, UK.
| | | | - Darren Plant
- NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust and University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
| | - Anne Barton
- Arthritis Research UK, Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, the University of Manchester, Manchester, UK. .,NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust and University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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Maranville JC, Di Rienzo A. Combining genetic and nongenetic biomarkers to realize the promise of pharmacogenomics for inflammatory diseases. Pharmacogenomics 2015; 15:1931-40. [PMID: 25495413 DOI: 10.2217/pgs.14.129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many drugs used to treat inflammatory diseases are ineffective in a substantial proportion of patients. Identifying patients that are likely to respond to specific therapies would facilitate personalized treatment strategies that could improve outcomes while reducing costs and risks of adverse events. Despite these clear benefits, there are limited examples of predictive biomarkers of drug efficacy currently implemented into clinical practice for inflammatory diseases. We review efforts to identify genetic and nongenetic biomarkers of drug response in these diseases and consider potential benefits from combining multiple sources of biological data into multifeature predictive models.
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Affiliation(s)
- Joseph C Maranville
- Committee on Clinical Pharmacology & Pharmacogenomics, The University of Chicago, Chicago, IL, USA
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Response to Infliximab in Crohn's Disease: Genetic Analysis Supporting Expression Profile. Mediators Inflamm 2015; 2015:318207. [PMID: 26339133 PMCID: PMC4539178 DOI: 10.1155/2015/318207] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/11/2015] [Accepted: 03/11/2015] [Indexed: 12/19/2022] Open
Abstract
Substantial proportion of Crohn's disease (CD) patients shows no response or a limited response to treatment with infliximab (IFX) and to identify biomarkers of response would be of great clinical and economic benefit. The expression profile of five genes (S100A8-S100A9, G0S2, TNFAIP6, and IL11) reportedly predicted response to IFX and we aimed at investigating their etiologic role through genetic association analysis. Patients with active CD (350) who received at least three induction doses of IFX were included and classified according to IFX response. A tagging strategy was used to select genetic polymorphisms that cover the variability present in the chromosomal regions encoding the identified genes with altered expression. Following genotyping, differences between responders and nonresponders to IFX were observed in haplotypes of the studied regions: S100A8-S100A9 (rs11205276*G/rs3014866*C/rs724781*C/rs3006488*A; P = 0.05); G0S2 (rs4844486*A/rs1473683*T; P = 0.15); TNFAIP6 (rs11677200*C/rs2342910*A/rs3755480*G/rs10432475*A; P = 0.10); and IL11 (rs1126760*C/rs1042506*G; P = 0.07). These differences were amplified in patients with colonic and ileocolonic location for all but the TNFAIP6 haplotype, which evidenced significant difference in ileal CD patients. Our results support the role of the reported expression signature as predictive of anti-TNF outcome in CD patients and suggest an etiological role of those top-five genes in the IFX response pathway.
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McKinney EF, Lee JC, Jayne DRW, Lyons PA, Smith KGC. T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection. Nature 2015; 523:612-6. [PMID: 26123020 PMCID: PMC4623162 DOI: 10.1038/nature14468] [Citation(s) in RCA: 456] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/10/2015] [Indexed: 12/30/2022]
Abstract
The clinical course of autoimmune and infectious disease varies greatly, even between individuals with the same condition. An understanding of the molecular basis for this heterogeneity could lead to significant improvements in both monitoring and treatment. During chronic infection the process of T-cell exhaustion inhibits the immune response, facilitating viral persistence. Here we show that a transcriptional signature reflecting CD8 T-cell exhaustion is associated with poor clearance of chronic viral infection, but conversely predicts better prognosis in multiple autoimmune diseases. The development of CD8 T-cell exhaustion during chronic infection is driven both by persistence of antigen and by a lack of accessory 'help' signals. In autoimmunity, we find that where evidence of CD4 T-cell co-stimulation is pronounced, that of CD8 T-cell exhaustion is reduced. We can reproduce the exhaustion signature by modifying the balance of persistent stimulation of T-cell antigen receptors and specific CD2-induced co-stimulation provided to human CD8 T cells in vitro, suggesting that each process plays a role in dictating outcome in autoimmune disease. The 'non-exhausted' T-cell state driven by CD2-induced co-stimulation is reduced by signals through the exhaustion-associated inhibitory receptor PD-1, suggesting that induction of exhaustion may be a therapeutic strategy in autoimmune and inflammatory disease. Using expression of optimal surrogate markers of co-stimulation/exhaustion signatures in independent data sets, we confirm an association with good clinical outcome or response to therapy in infection (hepatitis C virus) and vaccination (yellow fever, malaria, influenza), but poor outcome in autoimmune and inflammatory disease (type 1 diabetes, anti-neutrophil cytoplasmic antibody-associated vasculitis, systemic lupus erythematosus, idiopathic pulmonary fibrosis and dengue haemorrhagic fever). Thus, T-cell exhaustion plays a central role in determining outcome in autoimmune disease and targeted manipulation of this process could lead to new therapeutic opportunities.
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Affiliation(s)
- Eoin F McKinney
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - James C Lee
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - David R W Jayne
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Paul A Lyons
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Kenneth G C Smith
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
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Thomson TM, Lescarbeau RM, Drubin DA, Laifenfeld D, de Graaf D, Fryburg DA, Littman B, Deehan R, Van Hooser A. Blood-based identification of non-responders to anti-TNF therapy in rheumatoid arthritis. BMC Med Genomics 2015; 8:26. [PMID: 26036272 PMCID: PMC4455917 DOI: 10.1186/s12920-015-0100-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/18/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Faced with an increasing number of choices for biologic therapies, rheumatologists have a critical need for better tools to inform rheumatoid arthritis (RA) disease management. The ability to identify patients who are unlikely to respond to first-line biologic anti-TNF therapies prior to their treatment would allow these patients to seek alternative therapies, providing faster relief and avoiding complications of disease. METHODS We identified a gene expression classifier to predict, pre-treatment, which RA patients are unlikely to respond to the anti-TNF infliximab. The classifier was trained and independently evaluated using four published whole blood gene expression data sets, in which RA patients (n = 116 = 44 + 15 + 30 + 27) were treated with infliximab, and their response assessed 14-16 months post treatment according to the European League Against Rheumatism (EULAR) response criteria. For each patient, prior knowledge was used to group gene expression measurements into disease-relevant biological signaling mechanisms that were used as the input features for regularized logistic regression. RESULTS The classifier produced a substantial enrichment of non-responders (59 %, given by the cross validated test precision) compared to the full population (27 % non-responders), while identifying nearly a third of non-responders. Given this classifier performance, treatment of predicted non-responders with alternative biologics would decrease their chance of non-response by between a third and a half, substantially improving their odds of effective treatment and stemming further disease progression. The classifier consisted of 18 signaling mechanisms, which together indicated that higher inflammatory signaling mediated by TNF and other cytokines was present pre-treatment in the blood of patients who responded to infliximab treatment. In contrast, non-responders were classified by relatively higher levels of specific metabolic activities in the blood prior to treatment. CONCLUSIONS We were able to successfully produce a classifier to identify a population of RA patients significantly enriched in anti-TNF non-responders across four different patient cohorts. Additional prospective studies are needed to validate and refine the classifier for clinical use.
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Affiliation(s)
| | | | | | | | | | | | - Bruce Littman
- Translational Medicine Associates, Stonington, CT, USA.
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Oliver J, Plant D, Webster AP, Barton A. Genetic and genomic markers of anti-TNF treatment response in rheumatoid arthritis. Biomark Med 2015; 9:499-512. [DOI: 10.2217/bmm.15.18] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite the success of anti-TNF drugs in the treatment of rheumatoid arthritis, a significant rate of nonresponse remains. Current clinical factors confer little power for predicting response and, in current practice, an unsatisfactory ‘trial and error’ approach governs therapeutic decisions. Candidate gene and unbiased genome-wide investigations have sought to identify genetic biomarkers that predict who will respond to anti-TNF drugs before the drug is administered. To date, few studies have yielded robust associations; herein, we discuss currently identified associations and the issues that need to be addressed in future investigations including insufficient power and an inadequate measure of disease activity. The potential for alternative predictors of anti-TNF therapy response from transcriptomic and epigenetic data will also be explored.
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Affiliation(s)
- James Oliver
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Institute of Inflammation & Repair, University Of Manchester, Manchester, M13 9PL, UK
| | - Darren Plant
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, Manchester, M13 9PL, UK
| | - Amy P Webster
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Institute of Inflammation & Repair, University Of Manchester, Manchester, M13 9PL, UK
| | - Anne Barton
- Arthritis Research UK Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Institute of Inflammation & Repair, University Of Manchester, Manchester, M13 9PL, UK
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, Manchester, M13 9PL, UK
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Ponchel F, Burska AN, Vital EM. Pharmacogenomics in rheumatoid arthritis: how close are we to the clinic? Pharmacogenomics 2015; 15:1275-9. [PMID: 25155929 DOI: 10.2217/pgs.14.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Frederique Ponchel
- Leeds Institute of Rheumatic & Musculoskeletal Medicine, University of Leeds, Leeds, UK
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Oswald M, Curran ME, Lamberth SL, Townsend RM, Hamilton JD, Chernoff DN, Carulli J, Townsend MJ, Weinblatt ME, Kern M, Pond CM, Lee A, Gregersen PK. Modular analysis of peripheral blood gene expression in rheumatoid arthritis captures reproducible gene expression changes in tumor necrosis factor responders. Arthritis Rheumatol 2015; 67:344-51. [PMID: 25371395 DOI: 10.1002/art.38947] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 10/30/2014] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To establish whether the analysis of whole-blood gene expression is useful in predicting or monitoring response to anti-tumor necrosis factor (anti-TNF) therapy in patients with rheumatoid arthritis (RA). METHODS Whole-blood RNA (using a PAXgene system to stabilize whole-blood RNA in the collection tube) was obtained at baseline and at 14 weeks from 3 independent cohorts, consisting of a combined total of 240 RA patients who were beginning therapy with anti-TNF. We used an approach to gene expression analysis that is based on modular patterns of gene expression, or modules. RESULTS Good and moderate responders according to the European League Against Rheumatism criteria exhibited highly significant and consistent changes in multiple gene expression modules after 14 weeks of therapy, as demonstrated by hypergeometric analysis. Strikingly, nonresponders exhibited very little change in any modules, despite exposure to TNF blockade. These patterns of change were highly consistent across all 3 cohorts, indicating that immunologic changes after TNF treatment are specific to the combination of both drug exposure and responder status. In contrast, modular patterns of gene expression did not exhibit consistent differences between responders and nonresponders at baseline in the 3 study cohorts. CONCLUSION These data provide evidence that using gene expression modules related to inflammatory disease may provide a valuable method for objective monitoring of the response of RA patients who are treated with TNF inhibitors.
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Affiliation(s)
- Michaela Oswald
- Feinstein Institute for Medical Research, Manhasset, New York
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de Jong TD, Vosslamber S, Verweij CL. Moving towards personalized medicine in rheumatoid arthritis. Arthritis Res Ther 2015; 16:110. [PMID: 25166016 PMCID: PMC4060201 DOI: 10.1186/ar4565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/12/2014] [Indexed: 12/14/2022] Open
Abstract
To develop personalized medicine strategies for improvement of patient management in rheumatoid arthritis, the clinical and molecular properties of the individual patients need to be well characterized. A crucial step in this approach is to discover subgroups of patients that are characterized by a good or poor treatment outcome. Dennis and colleagues have identified distinct pretreatment gene expression profiles in affected synovial tissue specimens and a tissue type-related systemic protein pattern which are associated with a positive or negative clinical outcome to monotherapy with adalumimab (anti-TNFα) and tocilizumab (anti-IL-6 receptor). These observations assign biological pathways associated with response outcome and provide evidence for the existence of systemic, easy-to-measure predictive biomarkers for clinical benefit of these biologics.
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MacIsaac KD, Baumgartner R, Kang J, Loboda A, Peterfy C, DiCarlo J, Riek J, Beals C. Pre-treatment whole blood gene expression is associated with 14-week response assessed by dynamic contrast enhanced magnetic resonance imaging in infliximab-treated rheumatoid arthritis patients. PLoS One 2014; 9:e113937. [PMID: 25504080 PMCID: PMC4264695 DOI: 10.1371/journal.pone.0113937] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 10/28/2014] [Indexed: 11/20/2022] Open
Abstract
Approximately 30% of rheumatoid arthritis patients achieve inadequate response to anti-TNF biologics. Attempts to identify molecular biomarkers predicting response have met with mixed success. This may be attributable, in part, to the variable and subjective disease assessment endpoints with large placebo effects typically used to classify patient response. Sixty-one patients with active RA despite methotrexate treatment, and with MRI-documented synovitis, were randomized to receive infliximab or placebo. Blood was collected at baseline and genome-wide transcription in whole blood was measured using microarrays. The primary endpoint in this study was determined by measuring the transfer rate constant (Ktrans) of a gadolinium-based contrast agent from plasma to synovium using MRI. Secondary endpoints included repeated clinical assessments with DAS28(CRP), and assessments of osteitis and synovitis by the RAMRIS method. Infliximab showed greater decrease from baseline in DCE-MRI Ktrans of wrist and MCP at all visits compared with placebo (P<0.001). Statistical analysis was performed to identify genes associated with treatment-specific 14-week change in Ktrans. The 256 genes identified were used to derive a gene signature score by averaging their log expression within each patient. The resulting score correlated with improvement of Ktrans in infliximab-treated patients and with deterioration of Ktrans in placebo-treated subjects. Poor responders showed high expression of activated B-cell genes whereas good responders exhibited a gene expression pattern consistent with mobilization of neutrophils and monocytes and high levels of reticulated platelets. This gene signature was significantly associated with clinical response in two previously published whole blood gene expression studies using anti-TNF therapies. These data provide support for the hypothesis that anti-TNF inadequate responders comprise a distinct molecular subtype of RA characterized by differences in pre-treatment blood mRNA expression. They also highlight the importance of placebo controls and robust, objective endpoints in biomarker discovery. Trial Registration: ClinicalTrials.gov NCT01313520
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Affiliation(s)
- Kenzie D. MacIsaac
- Merck & Co. Inc., Department of Genetics and Pharmacogenomics, Boston, Massachusetts, United States of America
- * E-mail:
| | - Richard Baumgartner
- Merck & Co. Inc., Department of Biometrics Research, Whitehouse Station, New Jersey, United States of America
| | - Jia Kang
- Merck & Co. Inc., Department of Biometrics Research, Whitehouse Station, New Jersey, United States of America
| | - Andrey Loboda
- Merck & Co. Inc., Department of Genetics and Pharmacogenomics, Boston, Massachusetts, United States of America
| | - Charles Peterfy
- Spire Sciences Inc., Boca Raton, Florida, United States of America
| | - Julie DiCarlo
- Spire Sciences Inc., Boca Raton, Florida, United States of America
| | - Jonathan Riek
- Virtual Scopics, Rochester, New York, United States of America
| | - Chan Beals
- Merck & Co. Inc., Clinical Research, Whitehouse Station, New Jersey, United States of America
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Gibson DS, Bustard MJ, McGeough CM, Murray HA, Crockard MA, McDowell A, Blayney JK, Gardiner PV, Bjourson AJ. Current and future trends in biomarker discovery and development of companion diagnostics for arthritis. Expert Rev Mol Diagn 2014; 15:219-34. [PMID: 25455156 DOI: 10.1586/14737159.2015.969244] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Musculoskeletal diseases such as rheumatoid arthritis are complex multifactorial disorders that are chronic in nature and debilitating for patients. A number of drug families are available to clinicians to manage these disorders but few tests exist to target these to the most responsive patients. As a consequence, drug failure and switching to drugs with alternate modes of action is common. In parallel, a limited number of laboratory tests are available which measure biological indicators or 'biomarkers' of disease activity, autoimmune status, or joint damage. There is a growing awareness that assimilating the fields of drug selection and diagnostic tests into 'companion diagnostics' could greatly advance disease management and improve outcomes for patients. This review aims to highlight: the current applications of biomarkers in rheumatology with particular focus on companion diagnostics; developments in the fields of proteomics, genomics, microbiomics, imaging and bioinformatics and how integration of these technologies into clinical practice could support therapeutic decisions.
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Affiliation(s)
- David S Gibson
- Northern Ireland Centre for Stratified Medicine, University of Ulster, C-TRIC Building, Altnagelvin Hospital campus, Glenshane Road, Londonderry, BT47 6SB, UK
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Gene expression profile predicting the response to anti-TNF treatment in patients with rheumatoid arthritis; analysis of GEO datasets. Joint Bone Spine 2014; 81:325-30. [DOI: 10.1016/j.jbspin.2014.01.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/15/2014] [Indexed: 01/10/2023]
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Sode J, Vogel U, Bank S, Andersen PS, Thomsen MK, Hetland ML, Locht H, Heegaard NHH, Andersen V. Anti-TNF treatment response in rheumatoid arthritis patients is associated with genetic variation in the NLRP3-inflammasome. PLoS One 2014; 9:e100361. [PMID: 24967817 PMCID: PMC4072633 DOI: 10.1371/journal.pone.0100361] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/23/2014] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Many patients with rheumatoid arthritis (RA) benefit from tumor necrosis factor-α blocking treatment (anti-TNF), but about one third do not respond. The objective of this study was to replicate and extend previously found associations between anti-TNF treatment response and genetic variation in the TNF-, NF-κB- and pattern recognition receptor signalling pathways. METHODS Forty-one single nucleotide polymorphisms (SNPs), including 34 functional, in 28 genes involved in inflammatory pathways were assessed in 538 anti-TNF naive Danish RA patients with clinical data. Multivariable logistic regression analyses were performed to test associations between genotypes and treatment response at 3-6 months using the European League Against Rheumatism (EULAR) response criterion. American College of Rheumatology treatment response (ACR50) and relative change in 28-joint disease activity score (relDAS28) were used as secondary outcomes. Subgroup analyses were stratified according to smoking status, type of anti-TNF drug and IgM-Rheumatoid Factor (IgM-RF) status. False discovery rate (FDR) controlling was used to adjust for multiple testing. RESULTS Statistically significant associations with EULAR response were found for two SNPs in NLRP3(rs4612666) (OR (odds ratio) for good/moderate response = 0.64 (95% confidence interval: 0.44-0.95), p = 0.025, q = 0.95) and INFG(rs2430561) (OR = 0.40 (0.21-0.76), p = 0.005, q = 0.18) and among IgM-RF positive patients for TNFRS1A(rs4149570) (0.59 (0.36-0.98), p = 0.040, q = 0.76). Current smokers who carried the NLRP3(rs4612666) variant allele were less likely to benefit from anti-TNF treatment (OR = 0.24 (0.10-0.56), p = 0.001, q = 0.04). CONCLUSIONS In a population of Danish RA patients, we confirm the NLRP3 gene as associated with EULAR anti-TNF response as previously reported. The NLRP3 variant (T) allele is associated with lower treatment response, in particular among current smokers. Furthermore, we find that a functional polymorphism in the interferon-γ gene is associated with anti-TNF response. All findings should be tested by replication in independent validation cohorts and augmented by assessing cytokine levels and activities of the relevant gene products.
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Affiliation(s)
- Jacob Sode
- Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, Copenhagen, Denmark
- Department of Rheumatology, Frederiksberg Hospital, Frederiksberg, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Steffen Bank
- Department of Medicine, Viborg Regional Hospital, Viborg, Denmark
- Biomedicine, University of Aarhus, Aarhus, Denmark
| | - Paal Skytt Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | - Merete Lund Hetland
- The DANBIO Registry, Copenhagen Center for Arthritis Research, Center for Rheumatology and Spine Diseases, Glostrup Hospital, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henning Locht
- Department of Rheumatology, Frederiksberg Hospital, Frederiksberg, Denmark
| | - Niels H. H. Heegaard
- Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Vibeke Andersen
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Medicine, Viborg Regional Hospital, Viborg, Denmark
- Organ Center, Hospital of Southern Jutland, Aabenraa, Denmark
- OPEN (Odense Patient data Explorative Network), Odense University Hospital, Odense, Denmark
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Sanayama Y, Ikeda K, Saito Y, Kagami SI, Yamagata M, Furuta S, Kashiwakuma D, Iwamoto I, Umibe T, Nawata Y, Matsumura R, Sugiyama T, Sueishi M, Hiraguri M, Nonaka K, Ohara O, Nakajima H. Prediction of Therapeutic Responses to Tocilizumab in Patients With Rheumatoid Arthritis: Biomarkers Identified by Analysis of Gene Expression in Peripheral Blood Mononuclear Cells Using Genome-Wide DNA Microarray. Arthritis Rheumatol 2014; 66:1421-31. [DOI: 10.1002/art.38400] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/04/2014] [Indexed: 01/13/2023]
Affiliation(s)
| | - Kei Ikeda
- Chiba University Hospital; Chiba Japan
| | | | - Shin-ichiro Kagami
- Chiba University Hospital, Chiba, Japan, and Asahi General Hospital; Asahi Japan
| | - Mieko Yamagata
- Chiba University Hospital, Chiba, Japan, and Asahi General Hospital; Asahi Japan
| | - Shunsuke Furuta
- Chiba University Hospital, Chiba, Japan, and Asahi General Hospital; Asahi Japan
| | | | | | | | | | | | - Takao Sugiyama
- National Hospital Organization Shimoshizu Hospital; Yotsukaido Japan
| | - Makoto Sueishi
- National Hospital Organization Shimoshizu Hospital; Yotsukaido Japan
| | | | - Ken Nonaka
- Kazusa DNA Research Institute; Kisarazu Japan
| | - Osamu Ohara
- Kazusa DNA Research Institute; Kisarazu Japan
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Burska AN, Roget K, Blits M, Soto Gomez L, van de Loo F, Hazelwood LD, Verweij CL, Rowe A, Goulielmos GN, van Baarsen LGM, Ponchel F. Gene expression analysis in RA: towards personalized medicine. THE PHARMACOGENOMICS JOURNAL 2014; 14:93-106. [PMID: 24589910 PMCID: PMC3992869 DOI: 10.1038/tpj.2013.48] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/26/2013] [Indexed: 12/13/2022]
Abstract
Gene expression has recently been at the forefront of advance in personalized medicine, notably in the field of cancer and transplantation, providing a rational for a similar approach in rheumatoid arthritis (RA). RA is a prototypic inflammatory autoimmune disease with a poorly understood etiopathogenesis. Inflammation is the main feature of RA; however, many biological processes are involved at different stages of the disease. Gene expression signatures offer management tools to meet the current needs for personalization of RA patients' care. This review analyses currently available information with respect to RA diagnostic, prognostic and prediction of response to therapy with a view to highlight the abundance of data, whose comparison is often inconclusive due to the mixed use of material source, experimental methodologies and analysis tools, reinforcing the need for harmonization if gene expression signatures are to become a useful clinical tool in personalized medicine for RA patients.
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Affiliation(s)
- A N Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and Leeds Musculoskeletal Biomediacal Research Unit, The University of Leeds, Leeds, UK
| | - K Roget
- TcLand Expression, Huningue, France
| | - M Blits
- Department of Pathology and Rheumatology, Inflammatory Disease Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
| | - L Soto Gomez
- School of law, The University of Leeds, Leeds, UK
| | - F van de Loo
- Department of Rheumatology Research and Advanced Therapeutics, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - L D Hazelwood
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - C L Verweij
- Department of Pathology and Rheumatology, Inflammatory Disease Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
| | - A Rowe
- Janssen Research and Development, High Wycombe, UK
| | - G N Goulielmos
- Molecular Medicine and Human Genetics Section, Department of Medicine, University of Crete, Heraklion, Greece
| | - L G M van Baarsen
- Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - F Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and Leeds Musculoskeletal Biomediacal Research Unit, The University of Leeds, Leeds, UK
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The role of lymphotoxin signaling in the development of autoimmune pancreatitis and associated secondary extra-pancreatic pathologies. Cytokine Growth Factor Rev 2014; 25:125-37. [DOI: 10.1016/j.cytogfr.2014.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 12/23/2013] [Accepted: 01/02/2014] [Indexed: 12/24/2022]
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50
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Genomic and systems approaches to translational biomarker discovery in immunological diseases. Drug Discov Today 2013; 19:133-9. [PMID: 24126144 DOI: 10.1016/j.drudis.2013.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/13/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023]
Abstract
The high failure rate of new therapeutic mechanisms tested in clinical development has spurred an upsurge in research dedicated to discovering biomarker readouts that can improve decision-making. Increasingly, systems biology and genomic technologies, such as transcriptional profiling, are being leveraged to aid in the discovery of biomarker readouts. For inflammatory and immunological diseases, such as rheumatoid arthritis (RA) and asthma, progress has been made in developing biomarkers to monitor disease activity, prediction of response to therapy, and pharmacodynamic (PD) measurements. In this review, we discuss recent successes and challenges in these endeavors, highlighting the importance of human clinical studies of standard-of-care treatments in control subjects and patients with disease as the most direct path toward identifying useful translational biomarkers for clinical development.
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