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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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2
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Bessette L, Kinch CD. Drs. Bessette and Kinch reply. J Rheumatol 2023; 50:579-580. [PMID: 36243412 DOI: 10.3899/jrheum.220909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Louis Bessette
- L. Bessette, MD, MSc, Associate Professor, Department of Medicine, Laval University, Quebec City
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3
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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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5
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Birga AM, Ren L, Luo H, Zhang Y, Huang J. Prediction of New Risk Genes and Potential Drugs for Rheumatoid Arthritis from Multiomics Data. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:6783659. [PMID: 35140805 PMCID: PMC8820924 DOI: 10.1155/2022/6783659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/08/2021] [Accepted: 01/12/2022] [Indexed: 11/17/2022]
Abstract
Rheumatoid arthritis (RA) is an autoimmune and inflammatory disease for which there is a lack of therapeutic options. Genome-wide association studies (GWASs) have identified over 100 genetic loci associated with RA susceptibility; however, the most causal risk genes (RGs) associated with, and molecular mechanism underlying, RA remain unknown. In this study, we collected 95 RA-associated loci from multiple GWASs and detected 87 candidate high-confidence risk genes (HRGs) from these loci via integrated multiomics data (the genome-scale chromosome conformation capture data, enhancer-promoter linkage data, and gene expression data) using the Bayesian integrative risk gene selector (iRIGS). Analysis of these HRGs indicates that these genes were indeed, markedly associated with different aspects of RA. Among these, 36 and 46 HRGs have been reported to be related to RA and autoimmunity, respectively. Meanwhile, most novel HRGs were also involved in the significantly enriched RA-related biological functions and pathways. Furthermore, drug repositioning prediction of the HRGs revealed three potential targets (ERBB2, IL6ST, and MAPK1) and nine possible drugs for RA treatment, of which two IL-6 receptor antagonists (tocilizumab and sarilumab) have been approved for RA treatment and four drugs (trastuzumab, lapatinib, masoprocol, and arsenic trioxide) have been reported to have a high potential to ameliorate RA. In summary, we believe that this study provides new clues for understanding the pathogenesis of RA and is important for research regarding the mechanisms underlying RA and the development of therapeutics for this condition.
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Affiliation(s)
- Anteneh M. Birga
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Liping Ren
- School of Health Care Technology, Chengdu Neusoft University, Chengdu, China
| | - Huaichao Luo
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
- Department of Clinical Laboratory, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Yang Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
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6
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Aluko A, Ranganathan P. Pharmacogenetics of Drug Therapies in Rheumatoid Arthritis. Methods Mol Biol 2022; 2547:527-567. [PMID: 36068476 DOI: 10.1007/978-1-0716-2573-6_19] [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] [Indexed: 06/15/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic systemic inflammatory disorder that can lead to severe joint damage and is often associated with a high morbidity and disability. Disease-modifying anti-rheumatic drugs (DMARDs) are the mainstay of treatment in RA. DMARDs not only relieve the clinical signs and symptoms of RA but also inhibit the radiographic progression of disease and reduce the effects of chronic systemic inflammation. Since the introduction of biologic DMARDs in the late 1990s, the therapeutic range of options for the management of RA has significantly expanded. However, patients' response to these agents is not uniform with considerable variability in both efficacy and toxicity. There are no reliable means of predicting an individual patient's response to a given DMARD prior to initiation of therapy. In this chapter, the current published literature on the pharmacogenetics of traditional DMARDS and the newer biologic DMARDs in RA is highlighted. Pharmacogenetics may help individualize drug therapy in patients with RA by providing reliable biomarkers to predict medication toxicity and efficacy.
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Affiliation(s)
- Atinuke Aluko
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Prabha Ranganathan
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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7
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Ota M, Fujio K. Multi-omics approach to precision medicine for immune-mediated diseases. Inflamm Regen 2021; 41:23. [PMID: 34332645 PMCID: PMC8325815 DOI: 10.1186/s41232-021-00173-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/26/2021] [Indexed: 12/23/2022] Open
Abstract
Recent innovation in high-throughput sequencing technologies has drastically empowered the scientific research. Consequently, now, it is possible to capture comprehensive profiles of samples at multiple levels including genome, epigenome, and transcriptome at a time. Applying these kinds of rich information to clinical settings is of great social significance. For some traits such as cardiovascular diseases, attempts to apply omics datasets in clinical practice for the prediction of the disease risk have already shown promising results, although still under way for immune-mediated diseases. Multiple studies have tried to predict treatment response in immune-mediated diseases using genomic, transcriptomic, or clinical information, showing various possible indicators. For better prediction of treatment response or disease outcome in immune-mediated diseases, combining multi-layer information together may increase the power. In addition, in order to efficiently pick up meaningful information from the massive data, high-quality annotation of genomic functions is also crucial. In this review, we discuss the achievement so far and the future direction of multi-omics approach to immune-mediated diseases.
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Affiliation(s)
- Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan. .,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
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8
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Puentes-Osorio Y, Amariles P, Calleja MÁ, Merino V, Díaz-Coronado JC, Taborda D. Potential clinical biomarkers in rheumatoid arthritis with an omic approach. AUTOIMMUNITY HIGHLIGHTS 2021; 12:9. [PMID: 34059137 PMCID: PMC8165788 DOI: 10.1186/s13317-021-00152-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022]
Abstract
Objective To aid in the selection of the most suitable therapeutic option in patients with diagnosis of rheumatoid arthritis according to the phase of disease, through the review of articles that identify omics biological markers. Methods A systematic review in PubMed/Medline databases was performed. We searched articles from August 2014 to September 2019, in English and Spanish, filtered by title and full text; and using the terms "Biomarkers" AND “Rheumatoid arthritis". Results This article supplies an exhaustive review from research of objective measurement, omics biomarkers and how disease activity appraise decrease unpredictability in treatment determinations, and finally, economic, and clinical outcomes of treatment options by biomarkers’ potential influence. A total of 122 articles were included. Only 92 met the established criteria for review purposes and 17 relevant references about the topic were included as well. Therefore, it was possible to identify 196 potential clinical biomarkers: 22 non-omics, 20 epigenomics, 33 genomics, 21 transcriptomics, 78 proteomics, 4 glycomics, 1 lipidomics and 17 metabolomics. Conclusion A biomarker is a measurable indicator of some, biochemical, physiological, or morphological condition; evaluable at a molecular, biochemical, or cellular level. Biomarkers work as indicators of physiological or pathological processes, or as a result of a therapeutic management. In the last five years, new biomarkers have been identified, especially the omics, which are those that proceed from the investigation of genes (genomics), metabolites (metabolomics), and proteins (proteomics). These biomarkers contribute to the physician choosing the best therapeutic option in patients with rheumatoid arthritis.
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9
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Melville AR, Kearsley-Fleet L, Buch MH, Hyrich KL. Understanding Refractory Rheumatoid Arthritis: Implications for a Therapeutic Approach. Drugs 2021; 80:849-857. [PMID: 32361822 DOI: 10.1007/s40265-020-01309-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Refractory rheumatoid arthritis (RA) has emerged as an area of unmet need in a landscape of generally well-controlled disease. Whilst most patients are adequately treated on methotrexate and other first-line disease-modifying anti-rheumatic drugs (DMARDs), a proportion requires biologic (b) and targeted synthetic (ts) DMARDs, with a further subsection failing multiple agents. Recent observational studies have adopted working definitions of refractory RA based on number of failed DMARDs, with prevalence estimates of 6-21% depending on threshold and study population. Risk factors include treatment delay, baseline disease activity and function, female gender, smoking, obesity and lower socioeconomic status. Practical and conceptual challenges in defining refractory RA arise from limitations of disease activity scores used to assess response, with attendant misclassification risk of co-existent non-inflammatory pathology, and failure to capture additional outcomes, such as fatigue, that have variable treatment response. Time is an important factor in defining refractory disease; registry studies show that growing treatment options have resulted in rapid b/tsDMARD cycling and earlier refractory status, and refractory RA is itself a dynamic concept, evolving with each new therapeutic class. Whilst the biology underpinning refractory RA remains largely unknown, a general overview of biomarker studies and clinical trials old and new offers insights into prediction of response and treatment failure. Whilst the future holds promise, current data are insufficient to personalise or meaningfully sequence b/tsDMARDs. Therefore, avoidance of a refractory course is best achieved by following proven management paradigms (e.g. early diagnosis and treat-to-target), addressing modifiable risk factors, and considering enrolment in novel trials.
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Affiliation(s)
- Andrew R Melville
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Lianne Kearsley-Fleet
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Maya H Buch
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.,National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kimme L Hyrich
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK. .,National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK.
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10
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Gilani SS, Nair N, Plant D, Hyrich K, Morgan AW, Morris AP, Wilson AG, Isaacs JD, Barton A, Bluett J. Pharmacogenetics of TNF inhibitor response in rheumatoid arthritis utilizing the two-component disease activity score. Pharmacogenomics 2020; 21:1151-1156. [PMID: 33124499 PMCID: PMC7649675 DOI: 10.2217/pgs-2020-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: TNF inhibitor drugs are a treatment option for rheumatoid arthritis, but response is not universal. Response is typically measured using the composite 4-component (4C) disease activity score 28 (DAS28) which contains more subjective measures. This study used a validated 2-component (2C) DAS28 score to determine whether SNPs associated with response were replicated in the UK population. Materials & methods: A literature review identified TNF inhibitor response SNPs. Linear regression was conducted to replicate associations with 4C or 2C-DAS28 response. Results: Eighteen independent SNPs were analyzed in 1828 patients. One and four associations with 4C and 2C-DAS28 response respectively were identified (p ≤ 0.05). Conclusion: Further genetic associations were replicated using the 2C-DAS28 which may reflect the objective nature of 2C-AS28.
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Affiliation(s)
- Syed Sa Gilani
- School of Medicine, University of Manchester, Manchester, M13 9PT, UK
| | - Nisha Nair
- NIHR Manchester Biomedical Research Center, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, M13 9WL, UK.,Versus Arthritis Centre for Genetics & Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
| | - Darren Plant
- NIHR Manchester Biomedical Research Center, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, M13 9WL, UK.,Versus Arthritis Centre for Genetics & Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
| | - Kimme Hyrich
- NIHR Manchester Biomedical Research Center, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, M13 9WL, UK.,Versus Arthritis Center for Epidemiology, Center for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
| | - Ann W Morgan
- School of Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, LS2 9JT, UK
| | - Andrew P Morris
- Versus Arthritis Centre for Genetics & Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
| | - Anthony G Wilson
- School of Medicine & Medical Science, Conway Institute, University College Dublin, Dublin, Dublin 4, Ireland
| | - John D Isaacs
- Institute of Translational & Clinical Research, Newcastle University & Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 7RU, UK
| | - Anne Barton
- NIHR Manchester Biomedical Research Center, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, M13 9WL, UK.,Versus Arthritis Centre for Genetics & Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
| | - James Bluett
- NIHR Manchester Biomedical Research Center, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Center, Manchester, M13 9WL, UK.,Versus Arthritis Centre for Genetics & Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, M13 9PL, UK
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11
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Guan Y, Zhang H, Quang D, Wang Z, Parker SCJ, Pappas DA, Kremer JM, Zhu F. Machine Learning to Predict Anti-Tumor Necrosis Factor Drug Responses of Rheumatoid Arthritis Patients by Integrating Clinical and Genetic Markers. Arthritis Rheumatol 2019; 71:1987-1996. [PMID: 31342661 DOI: 10.1002/art.41056] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/18/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Accurate prediction of treatment responses in rheumatoid arthritis (RA) patients can provide valuable information on effective drug selection. Anti-tumor necrosis factor (anti-TNF) drugs are an important second-line treatment after methotrexate, the classic first-line treatment for RA. However, patient heterogeneity hinders identification of predictive biomarkers and accurate modeling of anti-TNF drug responses. This study was undertaken to investigate the usefulness of machine learning to assist in developing predictive models for treatment response. METHODS Using data on patient demographics, baseline disease assessment, treatment, and single-nucleotide polymorphism (SNP) array from the Dialogue on Reverse Engineering Assessment and Methods (DREAM): Rheumatoid Arthritis Responder Challenge, we created a Gaussian process regression model to predict changes in the Disease Activity Score in 28 joints (DAS28) for the patients and to classify them into either the responder or the nonresponder group. This model was developed and cross-validated using data from 1,892 RA patients. It was evaluated using an independent data set from 680 patients. We examined the effectiveness of the similarity modeling and the contribution of individual features. RESULTS In the cross-validation tests, our method predicted changes in DAS28 (ΔDAS28), with a correlation coefficient of 0.405. It correctly classified responses from 78% of patients. In the independent test, this method achieved a Pearson's correlation coefficient of 0.393 in predicting ΔDAS28. Gaussian process regression effectively remapped the feature space and identified subpopulations that do not respond well to anti-TNF treatments. Genetic SNP biomarkers showed small contributions in the prediction when added to the clinical models. This was the best-performing model in the DREAM Challenge. CONCLUSION The model described here shows promise in guiding treatment decisions in clinical practice, based primarily on clinical profiles with additional genetic information.
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Affiliation(s)
| | | | | | | | | | - Dimitrios A Pappas
- Columbia University College of Physicians and Surgeons, New York, New York, and Corrona LLC, Waltham, Massachusetts
| | - Joel M Kremer
- Corrona LLC, Waltham, Massachusetts, and Albany Medical College and The Center for Rheumatology, Albany, New York
| | - Fan Zhu
- Chinese Academy of Sciences, Chongqing, China
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12
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The impact of DNA methylation on the cancer proteome. PLoS Comput Biol 2019; 15:e1007245. [PMID: 31356589 PMCID: PMC6695193 DOI: 10.1371/journal.pcbi.1007245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/15/2019] [Accepted: 07/02/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant DNA methylation disrupts normal gene expression in cancer and broadly contributes to oncogenesis. We previously developed MethylMix, a model-based algorithmic approach to identify epigenetically regulated driver genes. MethylMix identifies genes where methylation likely executes a functional role by using transcriptomic data to select only methylation events that can be linked to changes in gene expression. However, given that proteins more closely link genotype to phenotype recent high-throughput proteomic data provides an opportunity to more accurately identify functionally relevant abnormal methylation events. Here we present a MethylMix analysis that refines nominations for epigenetic driver genes by leveraging quantitative high-throughput proteomic data to select only genes where DNA methylation is predictive of protein abundance. Applying our algorithm across three cancer cohorts we find that using protein abundance data narrows candidate nominations, where the effect of DNA methylation is often buffered at the protein level. Next, we find that MethylMix genes predictive of protein abundance are enriched for biological processes involved in cancer including functions involved in epithelial and mesenchymal transition. Moreover, our results are also enriched for tumor markers which are predictive of clinical features like tumor stage and we find clustering using MethylMix genes predictive of protein abundance captures cancer subtypes. To elucidate the molecular basis of cancer we examine the variation and dynamics characterizing the flow of information from epigenome to the transcriptome and proteome. Conducting the first genome wide analysis of epigenome-proteome associations, we present a MethylMix analysis that leverages protein abundance data taking advantage of recent high-throughput proteomic data generated using mass-spectrometry technology to elucidate the role of DNA methylation in cancer. By integrating across molecular data types, we confirm the benefit of using protein abundance data to provide additional insights into pathways and processes involved in oncogenesis and how they manifest as clinical phenotypes. Applying our method across three large cancer cohorts including breast cancer, ovarian cancer and colorectal cancer, MethylMix identifies key genes and describes molecular features and subtypes in these cancers.
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Acosta-Herrera M, González-Serna D, Martín J. The Potential Role of Genomic Medicine in the Therapeutic Management of Rheumatoid Arthritis. J Clin Med 2019; 8:jcm8060826. [PMID: 31185701 PMCID: PMC6617101 DOI: 10.3390/jcm8060826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/28/2019] [Accepted: 06/06/2019] [Indexed: 01/14/2023] Open
Abstract
During the last decade, important advances have occurred regarding understanding of the pathogenesis and treatment of rheumatoid arthritis (RA). Nevertheless, response to treatment is not universal, and choosing among different therapies is currently based on a trial and error approach. The specific patient’s genetic background influences the response to therapy for many drugs: In this sense, genomic studies on RA have produced promising insights that could help us find an effective therapy for each patient. On the other hand, despite the great knowledge generated regarding the genetics of RA, most of the investigations performed to date have focused on identifying common variants associated with RA, which cannot explain the complete heritability of the disease. In this regard, rare variants could also contribute to this missing heritability as well as act as biomarkers that help in choosing the right therapy. In the present article, different aspects of genetics in the pathogenesis and treatment of RA are reviewed, from large-scale genomic studies to specific rare variant analyses. We also discuss the shared genetic architecture existing among autoimmune diseases and its implications for RA therapy, such as drug repositioning.
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Affiliation(s)
- Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Av. del Conocimiento 17. Armilla, 18016 Granada, Spain.
| | - David González-Serna
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Av. del Conocimiento 17. Armilla, 18016 Granada, Spain.
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Av. del Conocimiento 17. Armilla, 18016 Granada, Spain.
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14
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Menegatti S, Bianchi E, Rogge L. Anti-TNF Therapy in Spondyloarthritis and Related Diseases, Impact on the Immune System and Prediction of Treatment Responses. Front Immunol 2019; 10:382. [PMID: 30941119 PMCID: PMC6434926 DOI: 10.3389/fimmu.2019.00382] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/14/2019] [Indexed: 12/14/2022] Open
Abstract
Immune-mediated inflammatory diseases (IMIDs), such as spondyloarthritis (SpA), psoriasis, Crohn's disease (CD), and rheumatoid arthritis (RA) remain challenging illnesses. They often strike at a young age and cause lifelong morbidity, representing a considerable burden for the affected individuals and society. Pioneering studies have revealed the presence of a TNF-dependent proinflammatory cytokine cascade in several IMIDs, and the introduction of anti-TNF therapy 20 years ago has proven effective to reduce inflammation and clinical symptoms in RA, SpA, and other IMID, providing unprecedented clinical benefits and a valid alternative in case of failure or intolerable adverse effects of conventional disease-modifying antirheumatic drugs (DMARDs, for RA) or non-steroidal anti-inflammatory drugs (NSAIDs, for SpA). However, our understanding of how TNF inhibitors (TNFi) affect the immune system in patients is limited. This question is relevant because anti-TNF therapy has been associated with infectious complications. Furthermore, clinical efficacy of TNFi is limited by a high rate of non-responsiveness (30–40%) in RA, SpA, and other IMID, exposing a substantial fraction of patients to side-effects without clinical benefit. Despite the extensive use of TNFi, it is still not possible to determine which patients will respond to TNFi before treatment initiation. The recent introduction of antibodies blocking IL-17 has expanded the therapeutic options for SpA, as well as psoriasis and psoriatic arthritis. It is therefore essential to develop tools to guide treatment decisions for patients affected by SpA and other IMID, both to optimize clinical care and contain health care costs. After a brief overview of the biology of TNF, its receptors and currently used TNFi in the clinics, we summarize the progress that has been made to increase our understanding of the action of TNFi on the immune system in patients. We then summarize efforts dedicated to identify biomarkers that can predict treatment responses to TNFi and we conclude with a section dedicated to the recently introduced inhibitors of IL-17A and IL-23 in SpA and related diseases. The focus of this review is on SpA, however, we also refer to RA on topics for which only limited information is available on SpA in the literature.
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Affiliation(s)
- Silvia Menegatti
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Unité Mixte de Recherche, Institut Pasteur/AP-HP Hôpital Cochin, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Elisabetta Bianchi
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Unité Mixte de Recherche, Institut Pasteur/AP-HP Hôpital Cochin, Paris, France
| | - Lars Rogge
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Unité Mixte de Recherche, Institut Pasteur/AP-HP Hôpital Cochin, Paris, France
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15
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Evaluation of 12 GWAS-drawn SNPs as biomarkers of rheumatoid arthritis response to TNF inhibitors. A potential SNP association with response to etanercept. PLoS One 2019; 14:e0213073. [PMID: 30818333 PMCID: PMC6395028 DOI: 10.1371/journal.pone.0213073] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/14/2019] [Indexed: 12/14/2022] Open
Abstract
Research in rheumatoid arthritis (RA) is increasingly focused on the discovery of biomarkers that could enable personalized treatments. The genetic biomarkers associated with the response to TNF inhibitors (TNFi) are among the most studied. They include 12 SNPs exhibiting promising results in the three largest genome-wide association studies (GWAS). However, they still require further validation. With this aim, we assessed their association with response to TNFi in a replication study, and a meta-analysis summarizing all non-redundant data. The replication involved 755 patients with RA that were treated for the first time with a biologic drug, which was either infliximab (n = 397), etanercept (n = 155) or adalimumab (n = 203). Their DNA samples were successfully genotyped with a single-base extension multiplex method. Lamentably, none of the 12 SNPs was associated with response to the TNFi in the replication study (p > 0.05). However, a drug-stratified exploratory analysis revealed a significant association of the NUBPL rs2378945 SNP with a poor response to etanercept (B = -0.50, 95% CI = -0.82, -0.17, p = 0.003). In addition, the meta-analysis reinforced the previous association of three SNPs: rs2378945, rs12142623, and rs4651370. In contrast, five of the remaining SNPs were less associated than before, and the other four SNPs were no longer associated with the response to treatment. In summary, our results highlight the complexity of the pharmacogenetics of TNFi in RA showing that it could involve a drug-specific component and clarifying the status of the 12 GWAS-drawn SNPs.
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16
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A noncanonical role for the engulfment gene ELMO1 in neutrophils that promotes inflammatory arthritis. Nat Immunol 2019; 20:141-151. [PMID: 30643265 PMCID: PMC6402828 DOI: 10.1038/s41590-018-0293-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
Rheumatoid arthritis is characterized by progressive joint inflammation and affects ~1% of the human population. We noted single nucleotide polymorphisms (SNPs) in the apoptotic cell engulfment genes ELMO1, DOCK2, and RAC1 linked to rheumatoid arthritis. As ELMO1 promotes cytoskeletal reorganization during engulfment, we hypothesized that ELMO1 loss would worsen inflammatory arthritis. Surprisingly, Elmo1-deficient mice showed reduced joint inflammation in acute and chronic arthritis models. Genetic and cell biological studies revealed that ELMO1 associates with receptors linked to neutrophil function in arthritis and regulates activation and early neutrophil recruitment to the joints, without general inhibition of inflammatory responses. Further, neutrophils from peripheral blood of human donors that carry the SNP in ELMO1 associated with arthritis display increased migratory capacity, whereas ELMO1 knockdown reduces human neutrophil migration to chemokines linked to arthritis. These data identify ‘non-canonical’ roles for ELMO1 as an important cytoplasmic regulator of specific neutrophil receptors and promoter of arthritis.
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17
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Comparative study for haplotype block partitioning methods - Evidence from chromosome 6 of the North American Rheumatoid Arthritis Consortium (NARAC) dataset. PLoS One 2019; 13:e0209603. [PMID: 30596705 PMCID: PMC6312333 DOI: 10.1371/journal.pone.0209603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Haplotype-based methods compete with “one-SNP-at-a-time” approaches on being preferred for association studies. Chromosome 6 contains most of the known genetic biomarkers for rheumatoid arthritis (RA) disease. Therefore, chromosome 6 serves as a benchmark for the haplotype methods testing. The aim of this study is to test the North American Rheumatoid Arthritis Consortium (NARAC) dataset to find out if haplotype block methods or single-locus approaches alone can sufficiently provide the significant single nucleotide polymorphisms (SNPs) associated with RA. In addition, could we be satisfied with only one method of the haplotype block methods for partitioning chromosome 6 of the NARAC dataset? In the NARAC dataset, chromosome 6 comprises 35,574 SNPs for 2,062 individuals (868 cases, 1,194 controls). Individual SNP approach and three haplotype block methods were applied to the NARAC dataset to identify the RA biomarkers. We employed three haplotype partitioning methods which are confidence interval test (CIT), four gamete test (FGT), and solid spine of linkage disequilibrium (SSLD). P-values after stringent Bonferroni correction for multiple testing were measured to assess the strength of association between the genetic variants and RA susceptibility. Moreover, the block size (in base pairs (bp) and number of SNPs included), number of blocks, percentage of uncovered SNPs by the block method, percentage of significant blocks from the total number of blocks, number of significant haplotypes and SNPs were used to compare among the three haplotype block methods. Individual SNP, CIT, FGT, and SSLD methods detected 432, 1,086, 1,099, and 1,322 associated SNPs, respectively. Each method identified significant SNPs that were not detected by any other method (Individual SNP: 12, FGT: 37, CIT: 55, and SSLD: 189 SNPs). 916 SNPs were discovered by all the three haplotype block methods. 367 SNPs were discovered by the haplotype block methods and the individual SNP approach. The P-values of these 367 SNPs were lower than those of the SNPs uniquely detected by only one method. The 367 SNPs detected by all the methods represent promising candidates for RA susceptibility. They should be further investigated for the European population. A hybrid technique including the four methods should be applied to detect the significant SNPs associated with RA for chromosome 6 of the NARAC dataset. Moreover, SSLD method may be preferred for its favored benefits in case of selecting only one method.
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Affiliation(s)
- Mohamed N. Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia, Egypt
- * E-mail: ,
| | - Mai S. Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology (MUST), 6th of October City, Egypt
| | - Ayman M. Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G. Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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18
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Darden L, Kundu K, Pal LR, Moult J. Harnessing formal concepts of biological mechanism to analyze human disease. PLoS Comput Biol 2018; 14:e1006540. [PMID: 30586388 PMCID: PMC6306204 DOI: 10.1371/journal.pcbi.1006540] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mechanism is a widely used concept in biology. In 2017, more than 10% of PubMed abstracts used the term. Therefore, searching for and reasoning about mechanisms is fundamental to much of biomedical research, but until now there has been almost no computational infrastructure for this purpose. Recent work in the philosophy of science has explored the central role that the search for mechanistic accounts of biological phenomena plays in biomedical research, providing a conceptual basis for representing and analyzing biological mechanism. The foundational categories for components of mechanisms—entities and activities—guide the development of general, abstract types of biological mechanism parts. Building on that analysis, we have developed a formal framework for describing and representing biological mechanism, MecCog, and applied it to describing mechanisms underlying human genetic disease. Mechanisms are depicted using a graphical notation. Key features are assignment of mechanism components to stages of biological organization and classes; visual representation of uncertainty, ignorance, and ambiguity; and tight integration with literature sources. The MecCog framework facilitates analysis of many aspects of disease mechanism, including the prioritization of future experiments, probing of gene−drug and gene−environment interactions, identification of possible new drug targets, personalized drug choice, analysis of nonlinear interactions between relevant genetic loci, and classification of diseases based on mechanism.
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Affiliation(s)
- Lindley Darden
- Department of Philosophy, University of Maryland College Park, College Park, Maryland, United States of America
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland College Park, College Park, Maryland, United States of America
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, United States of America
- * E-mail:
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19
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Genome-wide association study of response to tumour necrosis factor inhibitor therapy in rheumatoid arthritis. THE PHARMACOGENOMICS JOURNAL 2018; 18:657-664. [PMID: 30166627 PMCID: PMC6150911 DOI: 10.1038/s41397-018-0040-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/05/2018] [Accepted: 05/11/2018] [Indexed: 12/30/2022]
Abstract
Rheumatoid arthritis (RA) is characterised by chronic synovial joint inflammation. Treatment has been revolutionised by tumour necrosis factor alpha inhibitors (TNFi) but each available drug shows a significant non-response rate. We conducted a genome-wide association study of 1752 UK RA TNFi-treated patients to identify predictors of change in the Disease Activity Score 28 (DAS28) and subcomponents over 3–6 months. The rs7195994 variant at the FTO gene locus was associated with infliximab response when looking at a change in the swollen joint count (SJC28) subcomponent (p = 9.74 × 10−9). Capture Hi-C data show chromatin interactions in GM12878 cells between rs2540767, in high linkage disequilibrium with rs7195994 (R2 = 0.9) and IRX3, a neighbouring gene of FTO. IRX3 encodes a transcription factor involved in adipocyte remodelling and is regarded as the obesity gene at the FTO locus. Importantly, the rs7195994 association remained significantly associated following adjustment for BMI. In addition, using capture Hi-C data we showed interactions between TNFi-response associated variants and 16 RA susceptibility variants.
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20
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Lopez-Rodriguez R, Perez-Pampin E, Marquez A, Blanco FJ, Joven B, Carreira P, Ferrer MA, Caliz R, Valor L, Narvaez J, Cañete JD, Ordoñez MDC, Manrique-Arija S, Vasilopoulos Y, Balsa A, Pascual-Salcedo D, Moreno-Ramos MJ, Alegre-Sancho JJ, Navarro-Sarabia F, Moreira V, Garcia-Portales R, Raya E, Magro-Checa C, Martin J, Gomez-Reino JJ, Gonzalez A. Validation study of genetic biomarkers of response to TNF inhibitors in rheumatoid arthritis. PLoS One 2018; 13:e0196793. [PMID: 29734345 PMCID: PMC5937760 DOI: 10.1371/journal.pone.0196793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 11/19/2022] Open
Abstract
Genetic biomarkers are sought to personalize treatment of patients with rheumatoid arthritis (RA), given their variable response to TNF inhibitors (TNFi). However, no genetic biomaker is yet sufficiently validated. Here, we report a validation study of 18 previously reported genetic biomarkers, including 11 from GWAS of response to TNFi. The validation was attempted in 581 patients with RA that had not been treated with biologic antirheumatic drugs previously. Their response to TNFi was evaluated at 3, 6 and 12 months in two ways: change in the DAS28 measure of disease activity, and according to the EULAR criteria for response to antirheumatic drugs. Association of these parameters with the genotypes, obtained by PCR amplification followed by single-base extension, was tested with regression analysis. These analyses were adjusted for baseline DAS28, sex, and the specific TNFi. However, none of the proposed biomarkers was validated, as none showed association with response to TNFi in our study, even at the time of assessment and with the outcome that showed the most significant result in previous studies. These negative results are notable because this was the first independent validation study for 12 of the biomarkers, and because they indicate that prudence is needed in the interpretation of the proposed biomarkers of response to TNFi even when they are supported by very low p values. The results also emphasize the requirement of independent replication for validation, and the need to search protocols that could increase reproducibility of the biomarkers of response to TNFi.
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Affiliation(s)
- Rosario Lopez-Rodriguez
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Eva Perez-Pampin
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Ana Marquez
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - Francisco J. Blanco
- Rheumatology Department, Instituto de Investigacion Biomedica–Complejo Hospitalario Universitario A Coruna, Coruna, Spain
| | | | | | - Miguel Angel Ferrer
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Rafael Caliz
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Lara Valor
- Rheumatology Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Javier Narvaez
- Department of Rheumatology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Juan D. Cañete
- Arthritis Unit, Rheumatology Dpt, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Maria del Carmen Ordoñez
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga Spain
| | - Sara Manrique-Arija
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga Spain
| | - Yiannis Vasilopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Alejandro Balsa
- Rheumatology Unit, Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), Hospital Universitario La Paz, Madrid, Spain
| | - Dora Pascual-Salcedo
- Department of Immunology, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | | | | | - Virginia Moreira
- Rheumatology Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | | | - Enrique Raya
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
| | - Cesar Magro-Checa
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - Juan J. Gomez-Reino
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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21
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Fonseka CY, Rao DA, Raychaudhuri S. Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis. Curr Opin Immunol 2017; 49:27-36. [PMID: 28888129 PMCID: PMC5705469 DOI: 10.1016/j.coi.2017.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/12/2017] [Indexed: 12/17/2022]
Abstract
CD4+ T cells have been long known to play an important role in the pathogenesis of rheumatoid arthritis (RA), but the specific cell populations and states that drive the disease have been challenging to identify with low dimensional single cell data and bulk assays. The advent of high dimensional single cell technologies-like single cell RNA-seq or mass cytometry-has offered promise to defining key populations, but brings new methodological and statistical challenges. Recent single cell profiling studies have revealed a broad diversity of cell types among CD4+ T cells, identifying novel populations that are expanded or altered in RA. Here, we will review recent findings on CD4+ T cell heterogeneity and RA that have come from single cell profiling studies and discuss the best practices for conducting these studies.
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Affiliation(s)
- Chamith Y Fonseka
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Technical Institute and Harvard University, Cambridge, MA 02138, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Deepak A Rao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Massachusetts Technical Institute and Harvard University, Cambridge, MA 02138, USA; Center for Data Sciences, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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22
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Romão VC, Vital EM, Fonseca JE, Buch MH. Right drug, right patient, right time: aspiration or future promise for biologics in rheumatoid arthritis? Arthritis Res Ther 2017; 19:239. [PMID: 29065909 PMCID: PMC5655983 DOI: 10.1186/s13075-017-1445-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Individualising biologic disease-modifying anti-rheumatic drugs (bDMARDs) to maximise outcomes and deliver safe and cost-effective care is a key goal in the management of rheumatoid arthritis (RA). Investigation to identify predictive tools of bDMARD response is a highly active and prolific area of research. In addition to clinical phenotyping, cellular and molecular characterisation of synovial tissue and blood in patients with RA, using different technologies, can facilitate predictive testing. This narrative review will summarise the literature for the available bDMARD classes and focus on where progress has been made. We will also look ahead and consider the increasing use of 'omics' technologies, the potential they hold as well as the challenges, and what is needed in the future to fully realise our ambition of personalised bDMARD treatment.
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Affiliation(s)
- Vasco C. Romão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Edward M. Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - João Eurico Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Maya H. Buch
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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23
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Bek S, Bojesen AB, Nielsen JV, Sode J, Bank S, Vogel U, Andersen V. Systematic review and meta-analysis: pharmacogenetics of anti-TNF treatment response in rheumatoid arthritis. THE PHARMACOGENOMICS JOURNAL 2017; 17:403-411. [PMID: 28607508 PMCID: PMC5637244 DOI: 10.1038/tpj.2017.26] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/08/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease that affects ~1% of the Caucasian population. Over the last decades, the availability of biological drugs targeting the proinflammatory cytokine tumour necrosis factor α, anti-TNF drugs, has improved the treatment of patients with RA. However, one-third of the patients do not respond to the treatment. We wanted to evaluate the status of pharmacogenomics of anti-TNF treatment. We performed a PubMed literature search and all studies reporting original data on associations between genetic variants and anti-TNF treatment response in RA patients were included and results evaluated by meta-analysis. In total, 25 single nucleotide polymorphisms were found to be associated with anti-TNF treatment response in RA (19 from genome-wide association studies and 6 from the meta-analyses), and these map to genes involved in T cell function, NFκB and TNF signalling pathways (including CTCN5, TEC, PTPRC, FCGR2A, NFKBIB, FCGR2A, IRAK3). Explorative prediction analyses found that biomarkers for clinical treatment selection are not yet available.
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Affiliation(s)
- S Bek
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - A B Bojesen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark.,Research Unit for E-mental Health, Mental Health Services in the Region of Southern Odense, Odense, Denmark
| | - J V Nielsen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - J Sode
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - S Bank
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - U Vogel
- Research Unit for E-mental Health, Mental Health Services in the Region of Southern Odense, Odense, Denmark.,National Research Centre for the Working Environment, Copenhagen, Denmark
| | - V Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.,Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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24
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Xie X, Li F, Li S, Tian J, Chen JW, Du JF, Mao N, Chen J. Application of omics in predicting anti-TNF efficacy in rheumatoid arthritis. Clin Rheumatol 2017; 37:13-23. [PMID: 28600618 DOI: 10.1007/s10067-017-3639-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/11/2017] [Accepted: 04/13/2017] [Indexed: 12/16/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by progressive joint erosion. Tumor necrosis factor (TNF) antagonists are the most widely used biological disease-modifying anti-rheumatic drug in RA. However, there continue to be one third of RA patients who have poor or no response to TNF antagonists. Following consideration of the uncertainty of therapeutic effects and the high price of TNF antagonists, it is worthy to predict the treatment responses before anti-TNF therapy. According to the comparisons between the responders and non-responders to TNF antagonists by omic technologies, such as genomics, transcriptomics, proteomics, and metabolomics, rheumatologists are eager to find significant biomarkers to predict the effect of TNF antagonists in order to optimize the personalized treatment in RA.
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Affiliation(s)
- Xi Xie
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Fen Li
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Shu Li
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jing Tian
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jin-Wei Chen
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jin-Feng Du
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ni Mao
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jian Chen
- Department of Rheumatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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25
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Viatte S, Barton A. Genetics of rheumatoid arthritis susceptibility, severity, and treatment response. Semin Immunopathol 2017; 39:395-408. [PMID: 28555384 PMCID: PMC5486781 DOI: 10.1007/s00281-017-0630-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 12/18/2022]
Abstract
A decade after the first genome-wide association study in rheumatoid arthritis (RA), a plethora of genetic association studies have been published on RA and its clinical or serological subtypes. We review the major milestones in the study of the genetic architecture of RA susceptibility, severity, and response to treatment. We set the scientific context necessary for non-geneticists to understand the potential clinical applications of human genetics and its significance for a stratified approach to the management of RA in the future.
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Affiliation(s)
- Sebastien Viatte
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Anne Barton
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academic Health Science Centre, Central Manchester University Hospitals NHS Foundation Trust, Grafton Street, Manchester, M13 9WL, UK
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26
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A genetic risk score composed of rheumatoid arthritis risk alleles, HLA-DRB1 haplotypes, and response to TNFi therapy - results from a Swedish cohort study. Arthritis Res Ther 2016; 18:288. [PMID: 27912794 PMCID: PMC5135751 DOI: 10.1186/s13075-016-1174-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/08/2016] [Indexed: 11/10/2022] Open
Abstract
Background To prevent debilitating and irreversible joint damage, rheumatoid arthritis (RA) is often treated with tumor necrosis factor inhibitor (TNFi), but many patients do not respond to this costly therapy. Few predictors for response are known, and it has been proposed that genetic factors which influence the development of RA may also influence disease severity and response to therapy. Several previous studies have attempted to confirm this but results remain inconclusive. We expand on previous studies by including more RA risk alleles, and maximize power by combining them into a genetic risk score. Method We linked genotyped RA patients from the Epidemiological Investigation of Rheumatoid Arthritis study to the Swedish Rheumatology Quality Register, identifying patients who started a TNFi as their first biological disease-modifying anti-rheumatic drug, with a return visit within 2–8 months after treatment start (N = 867). We calculated risk scores from 76 established RA risk SNPs, and four HLA-DRB1 amino acid positions, and tested whether risk scores or individual genetic risk factors could predict the European League Against Rheumatism (EULAR) response. Results We found no association between any of the risk scores or HLA-DRB1 haplotypes and EULAR response, neither overall nor stratified by anti-citrullinated protein/peptide antibody (ACPA) status. When evaluating each of the 76 SNPs, we found that the number of SNPs presenting significant associations was not higher than expected by chance (5/76 SNPs had p < 0.05 in ACPA-positive RA, 4/76 in ACPA-negative RA). Conclusion Overall, known RA risk SNPs do not predict response to TNFi, either individually or when combined into a risk score. This does not support the hypothesis that genes influencing RA onset would also influence its prognosis and treatment response. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-1174-z) contains supplementary material, which is available to authorized users.
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Anti-citrullinated peptide antibodies and their value for predicting responses to biologic agents: a review. Rheumatol Int 2016; 36:1043-63. [PMID: 27271502 DOI: 10.1007/s00296-016-3506-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022]
Abstract
Anti-citrullinated peptide antibodies (ACPAs) play an important pathogenic role both at the onset and during the disease course. These antibodies precede the clinical appearance of rheumatoid arthritis (RA) and are associated with a less favorable prognosis, both clinically and radiologically. The objective of this work was to conduct a comprehensive review of studies published through September 2015 of ACPAs' role as a predictor of the therapeutic response to the biological agents in RA patients. The review also includes summary of the biology and detection of ACPAs as well as ACPAs in relation to joint disease and CV disease and the possible role of seroconversion. The reviews of studies examining TNF inhibitors and tocilizumab yielded negative results. In the case of rituximab, the data indicated a greater probability of clinical benefit in ACPA(+) patients versus ACPA(-) patients, as has been previously described for rheumatoid factor. Nonetheless, the effect is discreet and heterogeneous. Another drug that may have greater effectiveness in ACPA(+) patients is abatacept. Some studies have suggested that the drug is more efficient in ACPA(+) patients and that those patients show greater drug retention. In a subanalysis of the AMPLE trial, patients with very high ACPA titers who were treated with abatacept had a statistically significant response compared to patients with lower titers. In summary, the available studies suggest that the presence of or high titers of ACPA may predict a better response to rituximab and/or abatacept. Evidence regarding TNFi and tocilizumab is lacking. However, there is a lack of studies with appropriate designs to demonstrate that some drugs are superior to others for ACPA(+) patients.
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Associations between PTPRC rs10919563 A/G and FCGR2A R131H polymorphisms and responsiveness to TNF blockers in rheumatoid arthritis: a meta-analysis. Rheumatol Int 2016; 36:837-44. [PMID: 27074847 DOI: 10.1007/s00296-016-3476-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/05/2016] [Indexed: 10/22/2022]
Abstract
We aimed to investigate whether the PTPRC rs10919563 A/G and Fc gamma receptor 2A (FCGR2A) R131H polymorphisms can predict the response to anti-TNF therapy in rheumatoid arthritis (RA) patients. We conducted a meta-analysis of studies on the association between the PTPRC rs10919563 A/G or the FCGR2A R131H polymorphism and responsiveness to anti-TNF therapy in RA patients. Eighteen studies (twelve on PTPRC and six on FCGR2A) from eight articles involving 3058 patients were considered in this meta-analysis. The meta-analysis showed a significant association between the PTPRC rs10919563 A allele and response to TNF-α blockers in RA. The OR of the PTPRC A allele was significantly lower in responders (OR = 0.584, 95 % CI = 0.409-0.835, P = 0.003). Meta-analysis revealed no association between the FCGR2A HH + HR genotype and responsiveness to TNF blockers in all study subjects (OR = 0.762, 95 % CI = 0.543-1.068, P = 0.115). However, stratification by TNF inhibitor type showed that the FCGR2A HH + HR genotype was associated with responsiveness to adalimumab (OR = 0.591, 95 % CI = 0.369-0.947, P = 0.029), but not infliximab and etanercept (OR = 0.929, 95 % CI = 0.354-2.440, P = 0.881; OR = 0.804, 95 % CI = 0.293-2.207, P = 0.673). The PTPRC rs10919563 A allele shows a poor response to anti-TNF therapy, and the FCGR2A HH + HR genotype shows a poor response to adalimumab for RA. Genotyping for these polymorphisms may be useful for predicting the response to TNF-α blockers with respect to personalized medicine.
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Abstract
TNF-blocking agents, non-biological disease-modifying anti-rheumatic drugs (nbDMARDs) and non-steroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed treatments in psoriatic arthritis. A large proportion of patients do not respond to these medications, although unfortunately clinically useful biomarkers that predict future response are currently lacking. Several candidate gene polymorphisms have been associated with responses to biologic therapies and nbDMARDs; however, replication and validation of these variants in large prospective psoriatic arthritis cohorts are required before translating these to clinical practice. In this review, we discuss the advances made in pharmacogenetics of treatment response in psoriatic arthritis to date, with focus on biologic therapies approved for use, nbDMARDs and NSAIDs, as well as outline emerging methodologies to obtain data that will help inform a future precision medicine approach in this condition.
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Affiliation(s)
- Meghna Jani
- Arthritis Research UK Centre for Genetics and Genomics; Centre for Musculoskeletal Research, University of Manchester, Room 2.704, Stopford Building, Oxford Road, Manchester, M13 9PT, UK,
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Honne K, Hallgrímsdóttir I, Wu C, Sebro R, Jewell NP, Sakurai T, Iwamoto M, Minota S, Jawaheer D. A longitudinal genome-wide association study of anti-tumor necrosis factor response among Japanese patients with rheumatoid arthritis. Arthritis Res Ther 2016; 18:12. [PMID: 26776603 PMCID: PMC4718049 DOI: 10.1186/s13075-016-0920-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022] Open
Abstract
Background Studies of Caucasian patients with rheumatoid arthritis (RA) to identify genetic biomarkers of anti-tumor necrosis factor (TNF) response have used response at a single time point as the phenotype with which single nucleotide polymorphism (SNP) associations have been tested. The findings have been inconsistent across studies. Among Japanese patients, only a few SNPs have been investigated. We report here the first genome-wide association study (GWAS) to identify genetic biomarkers of anti-TNF response among Japanese RA patients, using response at 2 time-points for a more reliable clinical phenotype over time. Methods Disease Activity Scores based on 28 joint counts (DAS28) were assessed at baseline (before initial therapy), and after 3 and 6 months in 487 Japanese RA patients starting anti-TNF therapy for the first time or switching to a new anti-TNF agent. A genome-wide panel of SNPs was genotyped and additional SNPs were imputed. Using change in DAS28 scores from baseline at both 3 (ΔDAS-3) and 6 months (ΔDAS-6) as the response phenotype, a longitudinal genome-wide association analysis was conducted using generalized estimating equations (GEE) models, adjusting for baseline DAS28, treatment duration, type of anti-TNF agent and concomitant methotrexate. Cross-sectional analyses were performed using multivariate linear regression models, with response from a single time point (ΔDAS-3 or ΔDAS-6) as phenotype; all other variables were the same as in the GEE models. Results In the GEE models, borderline significant association was observed at 3 chromosomal regions (6q15: rs284515, p = 6.6x10−7; 6q27: rs75908454, p = 6.3x10−7 and 10q25.3: rs1679568, p = 8.1x10−7), extending to numerous SNPs in linkage disequilibrium (LD) across each region. Potential candidate genes in these regions include MAP3K7, BACH2 (6q15), GFRA1 (10q25.3), and WDR27 (6q27). The association at GFRA1 replicates a previous finding from a Caucasian dataset. In the cross-sectional analyses, ΔDAS-6 was significantly associated with the 6q15 locus (rs284511, p = 2.5x10−8). No other significant or borderline significant associations were identified. Conclusion Three genomic regions demonstrated significant or borderline significant associations with anti-TNF response in our dataset of Japanese RA patients, including a locus previously associated among Caucasians. Using repeated measures of response as phenotype enhanced the power to detect these associations. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-0920-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyoko Honne
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | | | - Chunsen Wu
- Research Unit of Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Obstertics & Gynecology, Odense University Hospital, Odense, Denmark
| | - Ronnie Sebro
- Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Nicholas P Jewell
- School of Public Health, University of California, Berkeley, CA, 94720, USA
| | | | - Masahiro Iwamoto
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Seiji Minota
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Damini Jawaheer
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
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Seldin MF. The genetics of human autoimmune disease: A perspective on progress in the field and future directions. J Autoimmun 2015; 64:1-12. [PMID: 26343334 PMCID: PMC4628839 DOI: 10.1016/j.jaut.2015.08.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/23/2015] [Indexed: 12/18/2022]
Abstract
Progress in defining the genetics of autoimmune disease has been dramatically enhanced by large scale genetic studies. Genome-wide approaches, examining hundreds or for some diseases thousands of cases and controls, have been implemented using high throughput genotyping and appropriate algorithms to provide a wealth of data over the last decade. These studies have identified hundreds of non-HLA loci as well as further defining HLA variations that predispose to different autoimmune diseases. These studies to identify genetic risk loci are also complemented by progress in gene expression studies including definition of expression quantitative trait loci (eQTL), various alterations in chromatin structure including histone marks, DNase I sensitivity, repressed chromatin regions as well as transcript factor binding sites. Integration of this information can partially explain why particular variations can alter proclivity to autoimmune phenotypes. Despite our incomplete knowledge base with only partial definition of hereditary factors and possible functional connections, this progress has and will continue to facilitate a better understanding of critical pathways and critical changes in immunoregulation. Advances in defining and understanding functional variants potentially can lead to both novel therapeutics and personalized medicine in which therapeutic approaches are chosen based on particular molecular phenotypes and genomic alterations.
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Affiliation(s)
- Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA; Division of Rheumatology and Allergy, Department of Medicine, University of California, Davis, Tupper Hall Room 4453, Davis, CA 95616, USA.
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Genetic Polymorphisms of IL-17F and TRAF3IP2 Could Be Predictive Factors of the Long-Term Effect of Infliximab against Crohn's Disease. BIOMED RESEARCH INTERNATIONAL 2015; 2015:416838. [PMID: 26558270 PMCID: PMC4628975 DOI: 10.1155/2015/416838] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/27/2015] [Indexed: 12/18/2022]
Abstract
Background. We aimed to identify certain genes related to response to infliximab (IFX) and biomarkers to predict the IFX effect for Japanese Crohn's disease (CD) patients by performing an association study of single nucleotide polymorphisms (SNPs) in candidate genes in the interleukin- (IL-) 17 signaling pathway with response to IFX after 1 year of treatment. Methods. A total of 103 patients were divided into two groups, responders and nonresponders. Twenty-eight tag SNPs in 5 genes were genotyped. The frequencies of alleles and genotypes of each SNP were compared between responders and nonresponders in three different inheritance models. A genetic test was performed using a combination of the associated SNPs as biomarkers. Results. Multivariate logistic regression analysis indicated that the four variable factors, concomitant use of immunomodulators, penetrating disease, a G/G genotype of rs766748 in IL-17F, and a C/C or C/A genotype of rs1883136 in TRAF3IP2, independently contributed to response to IFX after 1 year of treatment. Genetic test using the polymorphisms of these genes perfectly predicted the responder and nonresponder CD patients with both concomitant use of immunomodulators and penetrating disease. Conclusion. IL17F and TRAF3IP2 are one of IFX-related genes, useful as biomarkers of IFX response, and may be target molecules for new therapeutic drugs.
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Abstract
The disease spectrum and natural course of Crohn's disease and ulcerative colitis are highly variable. The majority of Crohn's disease patients will require surgery at a certain stage in their disease compared to only a fraction of the ulcerative colitis patients. Similarly, some patients are destined to experience an indolent disease course while others will require early intensive therapy. Ideally, these subtypes of patients should be identified as early as possible with the help of reliable prognostic factors in order to guide personalized therapeutic decisions. In this review, the authors focused on the most relevant reports on the use of different prognostic factors to predict disease course, postoperative recurrence and response to therapy in patients with inflammatory bowel disease. The last 15 years have seen a wealth of novel genetic and serological markers of disease severity. Nevertheless, none of these markers have proven to be superior to careful clinical phenotyping and endoscopic features early in the disease course. Future attempts should apply an integrated approach that unites clinical, serological and (epi)genetic information with environmental influences, with a clear focus on the microbiome to ultimately identify molecular-based and clinically relevant subgroups.
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Ferreiro-Iglesias A, Montes A, Perez-Pampin E, Cañete JD, Raya E, Magro-Checa C, Vasilopoulos Y, Sarafidou T, Caliz R, Ferrer MA, Joven B, Carreira P, Balsa A, Pascual-Salcedo D, Blanco FJ, Moreno-Ramos MJ, Fernández-Nebro A, Ordóñez MC, Alegre-Sancho JJ, Narváez J, Navarro-Sarabia F, Moreira V, Valor L, García-Portales R, Marquez A, Martin J, Gómez-Reino JJ, Gonzalez A. Replication of PTPRC as genetic biomarker of response to TNF inhibitors in patients with rheumatoid arthritis. THE PHARMACOGENOMICS JOURNAL 2015; 16:137-40. [PMID: 25896535 DOI: 10.1038/tpj.2015.29] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/16/2015] [Accepted: 03/02/2015] [Indexed: 01/21/2023]
Abstract
Genetic biomarkers could be useful for orienting treatment of patients with rheumatoid arthritis (RA), but none has been convincingly validated yet. Putative biomarkers include 14 single nucleotide polymorphisms that have shown association with response to TNF inhibitors (TNFi) in candidate gene studies and that we assayed here in 755 RA patients. Three of them, in the PTPRC, IL10 and CHUK genes, were significantly associated with response to TNFi. The most significant result was obtained with rs10919563 in PTPRC, which is a confirmed RA susceptibility locus. Its RA risk allele was associated with improved response (B=0.33, P=0.006). This is the second independent replication of this biomarker (P=9.08 × 10(-8) in the combined 3003 RA patients). In this way, PTPRC has become the most replicated genetic biomarker of response to TNFi. In addition, the positive but weaker replication of IL10 and CHUK should stimulate further validation studies.
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Affiliation(s)
- A Ferreiro-Iglesias
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - A Montes
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - E Perez-Pampin
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - J D Cañete
- Rheumatology Unit, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - E Raya
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
| | - C Magro-Checa
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
| | - Y Vasilopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - T Sarafidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - R Caliz
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - M A Ferrer
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - B Joven
- Reumatology Department, Hospital 12 de Octubre, Madrid, Spain
| | - P Carreira
- Reumatology Department, Hospital 12 de Octubre, Madrid, Spain
| | - A Balsa
- Department of Rheumatology and Institute for Health Research (IdiPAZ), University Hospital La Paz. Madrid, Spain
| | - D Pascual-Salcedo
- Immunology Unit, Instituto de Investigación Hospital Universitario La Paz, Hospital Universitario La Paz, Madrid, Spain
| | - F J Blanco
- Servicio de Reumatología. Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain.,Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M J Moreno-Ramos
- Department of Rheumatology, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - A Fernández-Nebro
- UGC de Reumatología, Instituto deInvestigación Biomédica de Málaga (IBIMA), HRU de Málaga, Universidad de Málaga, Málaga, Spain
| | - M C Ordóñez
- UGC de Reumatología, Instituto deInvestigación Biomédica de Málaga (IBIMA), HRU de Málaga, Universidad de Málaga, Málaga, Spain
| | | | - J Narváez
- Department of Rheumatology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - F Navarro-Sarabia
- Rheumatology Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - V Moreira
- Rheumatology Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | - L Valor
- Rheumatology Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - R García-Portales
- Department of Rheumatology, Hospital Virgen de la Victoria, Málaga, Spain
| | - A Marquez
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - J Martin
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - J J Gómez-Reino
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain.,Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - A Gonzalez
- Laboratorio de Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria-Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
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TRAF1/C5 but not PTPRC variants are potential predictors of rheumatoid arthritis response to anti-tumor necrosis factor therapy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:490295. [PMID: 25834819 PMCID: PMC4365300 DOI: 10.1155/2015/490295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/26/2014] [Indexed: 12/29/2022]
Abstract
Background. The aim of our work was to replicate, in a Southern European population, the association reported in Northern populations between PTPRC locus and response to anti-tumor necrosis factor (anti-TNF) treatment in rheumatoid arthritis (RA). We also looked at associations between five RA risk alleles and treatment response. Methods. We evaluated associations between anti-TNF treatment responses assessed by DAS28 change and by EULAR response at six months in 383 Portuguese patients. Univariate and multivariate linear and logistic regression analyses were performed. In a second step to confirm our findings, we pooled our population with 265 Spanish patients. Results. No association was found between PTPRC rs10919563 allele and anti-TNF treatment response, neither in Portuguese modeling for several clinical variables nor in the overall population combining Portuguese and Spanish patients. The minor allele for RA susceptibility, rs3761847 SNP in TRAF1/C5 region, was associated with a poor response in linear and logistic univariate and multivariate regression analyses. No association was observed with the other allellic variants. Results were confirmed in the pooled analysis. Conclusion. This study did not replicate the association between PTPRC and the response to anti-TNF treatment in our Southern European population. We found that TRAF1/C5 risk RA variants potentially influence anti-TNF treatment response.
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Kaiser R, Tang LF, Taylor KE, Sterba K, Nititham J, Brown EE, Edberg JC, McGwin G, Alarcón GS, Ramsey-Goldman R, Reveille JD, Vilá LM, Petri M, Rauch J, Miller E, Mesznik K, Kwok PY, Kimberly RP, Salmon JE, Criswell LA. A polymorphism in TLR2 is associated with arterial thrombosis in a multiethnic population of patients with systemic lupus erythematosus. Arthritis Rheumatol 2014; 66:1882-7. [PMID: 24578102 PMCID: PMC4269184 DOI: 10.1002/art.38520] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 02/18/2014] [Indexed: 11/12/2022]
Abstract
OBJECTIVE Thrombosis is a serious complication of systemic lupus erythematosus (SLE). Studies that have investigated the genetics of thrombosis in SLE are limited. We undertook this study to assess the association of previously implicated candidate genes, particularly Toll-like receptor (TLR) genes, with pathogenesis of thrombosis. METHODS We genotyped 3,587 SLE patients from 3 multiethnic populations for 77 single-nucleotide polymorphisms (SNPs) in 10 genes, primarily in TLRs 2, 4, 7, and 9, and we also genotyped 64 ancestry-informative markers (AIMs). We first analyzed association with arterial and venous thrombosis in the combined population via logistic regression, adjusting for top principal components of the AIMs and other covariates. We also subjected an associated SNP, rs893629, to meta-analysis (after stratification by ethnicity and study population) to confirm the association and to test for study population or ethnicity effects. RESULTS In the combined analysis, the SNP rs893629 in the KIAA0922/TLR2 region was significantly associated with arterial thrombosis (logistic P = 6.4 × 10(-5) , false discovery rate P = 0.0044). Two additional SNPs in TLR2 were also suggestive: rs1816702 (logistic P = 0.002) and rs4235232 (logistic P = 0.009). In the meta-analysis by study population, the odds ratio (OR) for arterial thrombosis with rs893629 was 2.44 (95% confidence interval 1.58-3.76), without evidence for heterogeneity (P = 0.78). By ethnicity, the effect was most significant among African Americans (OR 2.42, P = 3.5 × 10(-4) ) and European Americans (OR 3.47, P = 0.024). CONCLUSION TLR2 gene variation is associated with thrombosis in SLE, particularly among African Americans and European Americans. There was no evidence of association among Hispanics, and results in Asian Americans were limited due to insufficient sample size. These results may help elucidate the pathogenesis of this important clinical manifestation.
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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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Márquez A, Ferreiro-Iglesias A, Dávila-Fajardo CL, Montes A, Pascual-Salcedo D, Perez-Pampin E, Moreno-Ramos MJ, García-Portales R, Navarro F, Moreira V, Magro C, Caliz R, Ferrer MA, Alegre-Sancho JJ, Joven B, Carreira P, Balsa A, Vasilopoulos Y, Sarafidou T, Cabeza-Barrera J, Narvaez J, Raya E, Cañete JD, Fernández-Nebro A, Ordóñez MDC, de la Serna AR, Magallares B, Gomez-Reino JJ, González A, Martín J. Lack of validation of genetic variants associated with anti-tumor necrosis factor therapy response in rheumatoid arthritis: a genome-wide association study replication and meta-analysis. Arthritis Res Ther 2014; 16:R66. [PMID: 24612463 PMCID: PMC4060376 DOI: 10.1186/ar4504] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/25/2014] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION In this study, our aim was to elucidate the role of four polymorphisms identified in a prior large genome-wide association study (GWAS) in which the investigators analyzed the responses of patients with rheumatoid arthritis (RA) to treatment with tumor necrosis factor inhibitors (TNFi). The authors of that study reported that the four genetic variants were significantly associated. However, none of the associations reached GWAS significance, and two subsequent studies failed to replicate these associations. METHODS The four polymorphisms (rs12081765, rs1532269, rs17301249 and rs7305646) were genotyped in a total of 634 TNFi-treated RA patients of Spanish Caucasian origin. Four outcomes were evaluated: changes in the Disease Activity Score in 28 joints (DAS28) after 6 and 12 months of treatment and classification according to the European League Against Rheumatism (EULAR) response criteria at the same time points. Association with DAS28 changes was assessed by linear regression using an additive genetic model. Contingency tables of genotype and allele frequencies between EULAR responder and nonresponder patients were compared. In addition, we combined our data with those of previously reported studies in a meta-analysis including 2,998 RA patients. RESULTS None of the four genetic variants showed an association with response to TNFi in any of the four outcomes analyzed in our Spanish patients. In addition, only rs1532269 yielded a suggestive association (P = 0.0033) with the response to TNFi when available data from previous studies were combined in the meta-analysis. CONCLUSION Our data suggest that the rs12081765, rs1532269, rs17301249 and rs7305646 genetic variants do not have a role as genetic predictors of TNFi treatment outcomes.
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Plant D, Wilson AG, Barton A. Genetic and epigenetic predictors of responsiveness to treatment in RA. Nat Rev Rheumatol 2014; 10:329-37. [PMID: 24535543 DOI: 10.1038/nrrheum.2014.16] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methotrexate and TNF-blocking agents are the DMARDs most commonly prescribed for the treatment of rheumatoid arthritis (RA). However, not all patients treated with these nonbiologic and biologic DMARDs respond satisfactorily and few predictors of treatment efficacy have been identified, despite the fact that these therapies have now been available for many years. Many studies have investigated genetic factors that might predict patient responsiveness to therapies used to treat RA, and epigenetic studies regarding response to treatment are expected to accumulate in the literature in the near future. Herein, we review the advances in identifying genetic and epigenetic predictors of therapeutic responses to methotrexate and/or TNF inhibitors in RA that have been made to date, and highlight important considerations for future studies, such as the need for an improved, preferably biological, outcome measure reflecting response to treatment.
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Affiliation(s)
- Darren Plant
- Arthritis Research UK Centre of Excellence for Musculoskeletal Genetics, Manchester Academy of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Anthony G Wilson
- School of Medicine & Medical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Anne Barton
- Arthritis Research UK Centre of Excellence for Musculoskeletal Genetics, Manchester Academy of Health Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Predictive factors of response to biological disease modifying antirheumatic drugs: towards personalized medicine. Mediators Inflamm 2014; 2014:386148. [PMID: 24523570 PMCID: PMC3913459 DOI: 10.1155/2014/386148] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/27/2013] [Indexed: 01/19/2023] Open
Abstract
Many therapies are now available for patients with rheumatoid arthritis (RA) who have an inadequate response to methotrexate including tumor necrosis factor inhibitors, abatacept, tocilizumab, and rituximab. Clinical response to drugs varies widely between individuals. A part of this variability is due to the characteristics of the patient such as age, gender, concomitant therapies, body mass index, or smoking status. Clinical response also depends on disease characteristics including disease activity and severity and presence of autoantibodies. Genetic background, cytokine levels, and immune cell phenotypes could also influence biological therapy response. This review summarizes the impact of all those parameters on response to biological therapies.
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Lack of association of variants previously associated with anti-TNF medication response in rheumatoid arthritis patients: results from a homogeneous Greek population. PLoS One 2013; 8:e74375. [PMID: 24040234 PMCID: PMC3769251 DOI: 10.1371/journal.pone.0074375] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/31/2013] [Indexed: 12/21/2022] Open
Abstract
Treatment strategies blocking tumor necrosis factor (anti-TNF) have proven very successful in patients with rheumatoid arthritis (RA), showing beneficial effects in approximately 50-60% of the patients. However, a significant subset of patients does not respond to anti-TNF agents, for reasons that are still unknown. The aim of this study was to validate five single nucleotide polymorphisms (SNPs) of PTPRC, CD226, AFF3, MyD88 and CHUK gene loci that have previously been reported to predict anti-TNF outcome. In addition, two markers of RA susceptibility, namely TRAF1/C5 and STAT4 were assessed, in a cohort of anti-TNF–treated RA patients, from the homogeneous Greek island of Crete, Greece. The RA patient cohort consisted of 183 patients treated with either of 3 anti-TNF biologic agents (infliximab, adalimumab and etanercept) from the Clinic of Rheumatology of the University Hospital of Crete. The SNPs were genotyped by TaqMan assays or following the Restriction Fragments Length Polymorphisms (RFLPs) approach. Disease activity score in 28 joints (DAS28) at baseline and after 6 months were available for all patients and analysis of good versus poor response at 6 months was performed for each SNP. None of the 7 genetic markers correlated with treatment response. We conclude that the gene polymorphisms under investigation are not strongly predictive of anti-TNF response in RA patients from Greece.
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Pappas DA, Oh C, Plenge RM, Kremer JM, Greenberg JD. Association of rheumatoid arthritis risk alleles with response to anti-TNF biologics: results from the CORRONA registry and meta-analysis. Inflammation 2013; 36:279-84. [PMID: 23007924 DOI: 10.1007/s10753-012-9544-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, we investigated whether genetic variants known to be related with susceptibility to rheumatoid arthritis (RA) are also associated with response to therapy with anti-tumor necrosis factor (anti-TNF) biologics; 233 patients enrolled in the Consortium of Rheumatology Researchers of North America (CORRONA) RA registry were studied. Findings were combined with results from an international collaborative study (N = 1,283) in a meta-analysis (N = 1,516). Multivariate models investigating the association between single nucleotide polymorphisms (SNPs) and change in RA disease activity were adjusted for age, gender, concomitant methotrexate, and baseline disease activity. In the CORRONA cohort, nominal associations with disease activity improvement were observed for the rs1980422 SNP of the CD28 gene in multivariate models (coefficient -0.377, p = 0.005) but were not significant after adjustment for multiple comparisons (q = 0.10). In the meta-analysis, the only SNP with nominal associations with change in DAS28 was the rs2812378 SNP of the CCL21 gene (coefficient 1.9195, p = 0.0068). This association was not significant after adjustment for multiple comparisons (q = 0.143). We conclude that the established RA risk alleles studied were not significantly associated with response to anti-TNF biologics in the CORRONA cohort or the meta-analysis.
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Affiliation(s)
- Dimitrios A Pappas
- Division of Rheumatology, Department of Medicine, New York Presbyterian Hospital, College of Physicians and Surgeons, Columbia University, P&S Building, Suite 10-455, New York, NY 10032, USA.
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Cui J, Stahl EA, Saevarsdottir S, Miceli C, Diogo D, Trynka G, Raj T, Mirkov MU, Canhao H, Ikari K, Terao C, Okada Y, Wedrén S, Askling J, Yamanaka H, Momohara S, Taniguchi A, Ohmura K, Matsuda F, Mimori T, Gupta N, Kuchroo M, Morgan AW, Isaacs JD, Wilson AG, Hyrich KL, Herenius M, Doorenspleet ME, Tak PP, Crusius JBA, van der Horst-Bruinsma IE, Wolbink GJ, van Riel PLCM, van de Laar M, Guchelaar HJ, Shadick NA, Allaart CF, Huizinga TWJ, Toes REM, Kimberly RP, Bridges SL, Criswell LA, Moreland LW, Fonseca JE, de Vries N, Stranger BE, De Jager PL, Raychaudhuri S, Weinblatt ME, Gregersen PK, Mariette X, Barton A, Padyukov L, Coenen MJH, Karlson EW, Plenge RM. Genome-wide association study and gene expression analysis identifies CD84 as a predictor of response to etanercept therapy in rheumatoid arthritis. PLoS Genet 2013; 9:e1003394. [PMID: 23555300 PMCID: PMC3610685 DOI: 10.1371/journal.pgen.1003394] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 01/13/2013] [Indexed: 12/21/2022] Open
Abstract
Anti-tumor necrosis factor alpha (anti-TNF) biologic therapy is a widely used treatment for rheumatoid arthritis (RA). It is unknown why some RA patients fail to respond adequately to anti-TNF therapy, which limits the development of clinical biomarkers to predict response or new drugs to target refractory cases. To understand the biological basis of response to anti-TNF therapy, we conducted a genome-wide association study (GWAS) meta-analysis of more than 2 million common variants in 2,706 RA patients from 13 different collections. Patients were treated with one of three anti-TNF medications: etanercept (n = 733), infliximab (n = 894), or adalimumab (n = 1,071). We identified a SNP (rs6427528) at the 1q23 locus that was associated with change in disease activity score (ΔDAS) in the etanercept subset of patients (P = 8 × 10(-8)), but not in the infliximab or adalimumab subsets (P>0.05). The SNP is predicted to disrupt transcription factor binding site motifs in the 3' UTR of an immune-related gene, CD84, and the allele associated with better response to etanercept was associated with higher CD84 gene expression in peripheral blood mononuclear cells (P = 1 × 10(-11) in 228 non-RA patients and P = 0.004 in 132 RA patients). Consistent with the genetic findings, higher CD84 gene expression correlated with lower cross-sectional DAS (P = 0.02, n = 210) and showed a non-significant trend for better ΔDAS in a subset of RA patients with gene expression data (n = 31, etanercept-treated). A small, multi-ethnic replication showed a non-significant trend towards an association among etanercept-treated RA patients of Portuguese ancestry (n = 139, P = 0.4), but no association among patients of Japanese ancestry (n = 151, P = 0.8). Our study demonstrates that an allele associated with response to etanercept therapy is also associated with CD84 gene expression, and further that CD84 expression correlates with disease activity. These findings support a model in which CD84 genotypes and/or expression may serve as a useful biomarker for response to etanercept treatment in RA patients of European ancestry.
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Affiliation(s)
- Jing Cui
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eli A. Stahl
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Saedis Saevarsdottir
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Corinne Miceli
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Dorothee Diogo
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Gosia Trynka
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Towfique Raj
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Maša Umiċeviċ Mirkov
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Helena Canhao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Chikashi Terao
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yukinori Okada
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Sara Wedrén
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johan Askling
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
- Clinical Epidemiology Unit, Department of Medicine, Karolinska Institute/Karolinska University Hospital, Stockholm, Sweden
| | - Hisashi Yamanaka
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Shigeki Momohara
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Atsuo Taniguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Namrata Gupta
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Manik Kuchroo
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Ann W. Morgan
- NIHR–Leeds Musculoskeletal Biomedical Research Unit and Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - John D. Isaacs
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle Upon Tyne, United Kingdom
| | - Anthony G. Wilson
- Rheumatology Unit, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Kimme L. Hyrich
- School of Translational Medicine, Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester, United Kingdom
| | - Marieke Herenius
- Department of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Marieke E. Doorenspleet
- Department of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Paul-Peter Tak
- Department of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - J. Bart A. Crusius
- Laboratory of Immunogenetics, Department of Pathology, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | | | - Gert Jan Wolbink
- Sanquin Research Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- School of Medicine and Biomedical Sciences, Sheffield University, Sheffield, United Kingdom
- Jan van Breemen Institute, Amsterdam, The Netherlands
| | - Piet L. C. M. van Riel
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Mart van de Laar
- Arthritis Center Twente, University Twente and Medisch Spectrum Twente, Enschede, The Netherlands
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nancy A. Shadick
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cornelia F. Allaart
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tom W. J. Huizinga
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Rene E. M. Toes
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - S. Louis Bridges
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Lindsey A. Criswell
- Rosalind Russell Medical Research Center for Arthritis, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Larry W. Moreland
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - João Eurico Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam, Amsterdam, The Netherlands
| | - Barbara E. Stranger
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Philip L. De Jager
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Michael E. Weinblatt
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Xavier Mariette
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Leonid Padyukov
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marieke J. H. Coenen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Elizabeth W. Karlson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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Mera-Varela A, Ferreiro-Iglesias A, Perez-Pampin E, Porto-Silva M, Gómez-Reino JJ, Gonzalez A. Ultrasonographic assessment of enthesitis in HLA-B27 positive patients with rheumatoid arthritis, a matched case-only study. PLoS One 2013; 8:e58616. [PMID: 23505543 PMCID: PMC3591382 DOI: 10.1371/journal.pone.0058616] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 02/05/2013] [Indexed: 01/22/2023] Open
Abstract
Introduction HLA-B27 has a modifier effect on the phenotype of multiple diseases, both associated and non-associated with it. Among these effects, an increased frequency of clinical enthesitis in patients with Rheumatoid Arthritis (RA) has been reported but never explored again. We aimed to replicate this study with a sensitive and quantitative assessment of enthesitis by using standardized ultrasonography (US). Methods The Madrid Sonography Enthesitis Index (MASEI) was applied to the US assessment of 41 HLA-B27 positive and 41 matched HLA-B27 negative patients with longstanding RA. Clinical characteristics including explorations aimed to evaluate spondyloarthrtitis and laboratory tests were also done. Results A significant degree of abnormalities in the entheses of the patients with RA were found, but the MASEI values, and each of its components including the Doppler signal, were similar in HLA-B27 positive and negative patients. An increase of the MASEI scores with age was identified. Differences in two clinical features were found: a lower prevalence of rheumatoid factor and a more common story of low back pain in the HLA-B27 positive patients than in the negative. The latter was accompanied by radiographic sacroiliitis in two HLA-B27 positive patients. No other differences were detected. Conclusion We have found that HLA-B27 positive patients with RA do not have more enthesitis as assessed with US than the patients lacking this HLA allele. However, HLA-B27 could be shaping the RA phenotype towards RF seronegativity and axial involvement.
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Affiliation(s)
- Antonio Mera-Varela
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Aida Ferreiro-Iglesias
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Eva Perez-Pampin
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Marisol Porto-Silva
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | - Juan J. Gómez-Reino
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Research Laboratory 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria – Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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Plenge RM, Bridges SL. Personalized medicine in rheumatoid arthritis: miles to go before we sleep. ACTA ACUST UNITED AC 2013; 63:590-3. [PMID: 21360486 DOI: 10.1002/art.30126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Umiċeviċ Mirkov M, Cui J, Vermeulen SH, Stahl EA, Toonen EJM, Makkinje RR, Lee AT, Huizinga TWJ, Allaart R, Barton A, Mariette X, Miceli CR, Criswell LA, Tak PP, de Vries N, Saevarsdottir S, Padyukov L, Bridges SL, van Schaardenburg DJ, Jansen TL, Dutmer EAJ, van de Laar MAFJ, Barrera P, Radstake TRDJ, van Riel PLCM, Scheffer H, Franke B, Brunner HG, Plenge RM, Gregersen PK, Guchelaar HJ, Coenen MJH. Genome-wide association analysis of anti-TNF drug response in patients with rheumatoid arthritis. Ann Rheum Dis 2012; 72:1375-81. [PMID: 23233654 DOI: 10.1136/annrheumdis-2012-202405] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Treatment strategies blocking tumour necrosis factor (anti-TNF) have proven very successful in patients with rheumatoid arthritis (RA). However, a significant subset of patients does not respond for unknown reasons. Currently, there are no means of identifying these patients before treatment. This study was aimed at identifying genetic factors predicting anti-TNF treatment outcome in patients with RA using a genome-wide association approach. METHODS We conducted a multistage, genome-wide association study with a primary analysis of 2 557 253 single-nucleotide polymorphisms (SNPs) in 882 patients with RA receiving anti-TNF therapy included through the Dutch Rheumatoid Arthritis Monitoring (DREAM) registry and the database of Apotheekzorg. Linear regression analysis of changes in the Disease Activity Score in 28 joints after 14 weeks of treatment was performed using an additive model. Markers with p<10(-3) were selected for replication in 1821 patients from three independent cohorts. Pathway analysis including all SNPs with p<10(-3) was performed using Ingenuity. RESULTS 772 markers showed evidence of association with treatment outcome in the initial stage. Eight genetic loci showed improved p value in the overall meta-analysis compared with the first stage, three of which (rs1568885, rs1813443 and rs4411591) showed directional consistency over all four cohorts studied. We were unable to replicate markers previously reported to be associated with anti-TNF outcome. Network analysis indicated strong involvement of biological processes underlying inflammatory response and cell morphology. CONCLUSIONS Using a multistage strategy, we have identified eight genetic loci associated with response to anti-TNF treatment. Further studies are required to validate these findings in additional patient collections.
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Affiliation(s)
- Maša Umiċeviċ Mirkov
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, , Nijmegen, The Netherlands
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You S, Cho CS, Lee I, Hood L, Hwang D, Kim WU. A systems approach to rheumatoid arthritis. PLoS One 2012; 7:e51508. [PMID: 23240033 PMCID: PMC3519858 DOI: 10.1371/journal.pone.0051508] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 11/01/2012] [Indexed: 01/13/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease that primarily attacks synovial joints. Despite the advances in diagnosis and treatment of RA, novel molecular targets are still needed to improve the accuracy of diagnosis and the therapeutic outcomes. Here, we present a systems approach that can effectively 1) identify core RA-associated genes (RAGs), 2) reconstruct RA-perturbed networks, and 3) select potential targets for diagnosis and treatments of RA. By integrating multiple gene expression datasets previously reported, we first identified 983 core RAGs that show RA dominant differential expression, compared to osteoarthritis (OA), in the multiple datasets. Using the core RAGs, we then reconstructed RA-perturbed networks that delineate key RA associated cellular processes and transcriptional regulation. The networks revealed that synovial fibroblasts play major roles in defining RA-perturbed processes, anti-TNF-α therapy restored many RA-perturbed processes, and 19 transcription factors (TFs) have major contribution to deregulation of the core RAGs in the RA-perturbed networks. Finally, we selected a list of potential molecular targets that can act as metrics or modulators of the RA-perturbed networks. Therefore, these network models identify a panel of potential targets that will serve as an important resource for the discovery of therapeutic targets and diagnostic markers, as well as providing novel insights into RA pathogenesis.
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Affiliation(s)
- Sungyong You
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang, Korea
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Non-MHC risk alleles in rheumatoid arthritis and in the syntenic chromosome regions of corresponding animal models. Clin Dev Immunol 2012; 2012:284751. [PMID: 23251214 PMCID: PMC3521484 DOI: 10.1155/2012/284751] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 08/13/2012] [Accepted: 09/30/2012] [Indexed: 11/29/2022]
Abstract
Rheumatoid arthritis (RA) is a polygenic autoimmune disease primarily affecting the synovial joints. Numerous animal models show similarities to RA in humans; some of them not only mimic the clinical phenotypes but also demonstrate the involvement of homologous genomic regions in RA. This paper compares corresponding non-MHC genomic regions identified in rodent and human genome-wide association studies (GWAS). To date, over 30 non-MHC RA-associated loci have been identified in humans, and over 100 arthritis-associated loci have been identified in rodent models of RA. The genomic regions associated with the disease are designated by the name(s) of the gene having the most frequent and consistent RA-associated SNPs or a function suggesting their involvement in inflammatory or autoimmune processes. Animal studies on rats and mice preferentially have used single sequence length polymorphism (SSLP) markers to identify disease-associated qualitative and quantitative trait loci (QTLs) in the genome of F2 hybrids of arthritis-susceptible and arthritis-resistant rodent strains. Mouse GWAS appear to be far ahead of rat studies, and significantly more mouse QTLs correspond to human RA risk alleles.
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Plant D, Prajapati R, Hyrich KL, Morgan AW, Wilson AG, Isaacs JD, Barton A. Replication of association of the PTPRC gene with response to anti-tumor necrosis factor therapy in a large UK cohort. ACTA ACUST UNITED AC 2012; 64:665-70. [PMID: 21952740 PMCID: PMC3427899 DOI: 10.1002/art.33381] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Objective Several rheumatoid arthritis (RA) susceptibility variants map close to genes involved in the tumor necrosis factor (TNF) signaling pathway, prompting the investigation of RA susceptibility variants in studies of predictors of response to TNF blockade. Based on a previously reported association of RA with the PTPRC genetic locus, the present study was undertaken to test established RA susceptibility variants, including PTPRC, in the prediction of response to TNF blockade in a large cohort of patients from the UK. Methods DNA was extracted from the blood of 1,115 UK patients with RA who were receiving anti-TNF biologic therapy. Samples were analyzed for 29 single-nucleotide polymorphisms (SNPs) previously established as RA susceptibility variants. In the primary analysis, the effect of each SNP on treatment response was assessed by linear regression, using an additive model, in which absolute change in the Disease Activity Score in 28 joints at 6 months of followup was the outcome measure. In a secondary analysis, logistic regression models were used to compare patients with a good treatment response (n = 274) to those with a poor response (n = 195), as defined using the European League Against Rheumatism response criteria. Results were combined with those from previous studies to confirm the findings by meta-analysis. Results The PTPRC rs10919563 SNP was associated with improved treatment response in both the primary analysis (regression coefficient 0.19, 95% confidence interval [95% CI] 0.09, 0.37; P = 0.04) and secondary analysis (odds ratio 0.62, 95% CI 0.40, 0.95; P = 0.03). A meta-analysis combining these data with the results from a previous study strengthened the evidence for association with the PTPRC SNP (P = 5.13 × 10−5). No convincing association of the treatment response with other candidate loci was detected. Conclusion Presence of the rs10919563 RA susceptibility variant at the PTPRC gene locus predicts improved response to anti-TNF biologic therapy. Fine-mapping studies are required to determine whether this SNP or another variant at the locus provides the greatest predictive accuracy for treatment response.
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Affiliation(s)
- Darren Plant
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester, UK
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