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Myasoedova E. Predicting treatment response to methotrexate: are we closer to solving the enigma? Rheumatology (Oxford) 2024; 63:1479-1480. [PMID: 38019954 PMCID: PMC11147535 DOI: 10.1093/rheumatology/kead622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/18/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Affiliation(s)
- Elena Myasoedova
- Division of Rheumatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
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2
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Sysojev AÖ, Saevarsdottir S, Diaz-Gallo LM, Silberberg GN, Alfredsson L, Klareskog L, Baecklund E, Björkman L, Kastbom A, Rantapää-Dahlqvist S, Turesson C, Jonsdottir I, Stefansson K, Frisell T, Padyukov L, Askling J, Westerlind H. Genome-wide investigation of persistence with methotrexate treatment in early rheumatoid arthritis. Rheumatology (Oxford) 2024; 63:1221-1229. [PMID: 37326842 PMCID: PMC11065441 DOI: 10.1093/rheumatology/kead301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/12/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
OBJECTIVES To investigate the influence of genetic factors on persistence with treatment of early RA with MTX monotherapy. METHODS We conducted a genome-wide association study (GWAS) in a sample of 3902 Swedish early-RA patients initiating MTX in DMARD monotherapy as their first-ever DMARD. The outcome, short- and long-term MTX treatment persistence, was defined as remaining on MTX at 1 and at 3 years, respectively, with no additional DMARDs added. As genetic predictors, we investigated individual SNPs, and then calculated a polygenic risk score (PRS) based on SNPs associated with RA risk. The SNP-based heritability of persistence was estimated overall and by RA serostatus. RESULTS No individual SNP reached genome-wide significance (P < 5 × 10-8), either for persistence at 1 year or at 3 years. The RA PRS was not significantly associated with MTX treatment persistence at 1 year [relative risk (RR) = 0.98 (0.96-1.01)] or at 3 years [RR = 0.96 (0.93-1.00)]. The heritability of MTX treatment persistence was estimated to be 0.45 (0.15-0.75) at 1 year and 0.14 (0-0.40) at 3 years. The results in seropositive RA were comparable with those in the analysis of RA overall, while heritability estimates and PRS RRs were attenuated towards the null in seronegative RA. CONCLUSION Despite being the largest GWAS on an MTX treatment outcome to date, no genome-wide significant associations were detected. The modest heritability observed, coupled with the broad spread of suggestively associated loci, indicate that genetic influence is of polygenic nature. Nevertheless, MTX monotherapy persistence was lower in patients with a greater genetic disposition, per the PRS, towards RA.
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Affiliation(s)
- Anton Öberg Sysojev
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- deCODE Genetics Inc, Reykjavik, Iceland
| | - Lina-Marcela Diaz-Gallo
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Gilad N Silberberg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine (IMM), Karolinska Institute, Stockholm, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Eva Baecklund
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lena Björkman
- Department of Rheumatology and Inflammation Research, University of Göteborg, Göteborg, Sweden
| | - Alf Kastbom
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Carl Turesson
- Department of Clinical Sciences, Malmö, Lund University, Malmö, Sweden
| | - Ingileif Jonsdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- deCODE Genetics Inc, Reykjavik, Iceland
| | - Kari Stefansson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- deCODE Genetics Inc, Reykjavik, Iceland
| | - Thomas Frisell
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Johan Askling
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Helga Westerlind
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
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3
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Lend K, Koopman FA, Lampa J, Jansen G, Hetland ML, Uhlig T, Nordström D, Nurmohamed M, Gudbjornsson B, Rudin A, Østergaard M, Heiberg MS, Sokka-Isler T, Hørslev-Petersen K, Haavardsholm EA, Grondal G, Twisk JWR, van Vollenhoven R. Methotrexate Safety and Efficacy in Combination Therapies in Patients With Early Rheumatoid Arthritis: A Post Hoc Analysis of a Randomized Controlled Trial. Arthritis Rheumatol 2024; 76:363-376. [PMID: 37846618 DOI: 10.1002/art.42730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
OBJECTIVE We investigated methotrexate safety and the influence of dose on efficacy outcomes in combination with three different biologic treatments and with active conventional treatment (ACT) in early rheumatoid arthritis (RA). METHODS This post hoc analysis included 812 treatment-naïve patients with early RA who were randomized (1:1:1:1) in the NORD-STAR trial to receive methotrexate in combination with ACT, certolizumab-pegol, abatacept, or tocilizumab. Methotrexate safety, doses, and dose effects on Clinical Disease Activity Index (CDAI) remission were assessed after 24 weeks of treatment. RESULTS Compared with ACT, the prevalence of methotrexate-associated side effects was higher when methotrexate was combined with tocilizumab (hazard ratio [HR] 1.48, 95% confidence interval [CI] 1.20-1.84) but not with certolizumab-pegol (HR 0.99, 95% CI 0.79-1.23) or with abatacept (HR 0.93, 95% CI 0.75-1.16). With ACT as the reference, the methotrexate dose was significantly lower when used in combination with tocilizumab (β -4.65, 95% CI -5.83 to -3.46; P < 0.001) or abatacept (β -1.15, 95% CI -2.27 to -0.03; P = 0.04), and it was numerically lower in combination with certolizumab-pegol (β -1.07, 95% CI -2.21 to 0.07; P = 0.07). Methotrexate dose reductions were not associated with decreased CDAI remission rates within any of the treatment combinations. CONCLUSION Methotrexate was generally well tolerated in combination therapies, but adverse events were a limiting factor in receiving the target dose of 25 mg/wk, and these were more frequent in combination with tocilizumab versus ACT. On the other hand, methotrexate dose reductions were not associated with decreased CDAI remission rates within any of the four treatment combinations at 24 weeks.
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Affiliation(s)
- Kristina Lend
- Amsterdam University Medical Centers, Amsterdam, the Netherlands, and Karolinska Institute, Stockholm, Sweden
| | - Frieda A Koopman
- Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jon Lampa
- Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Gerrit Jansen
- Vrije Universiteit Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Merete L Hetland
- Copenhagen University Hospital Rigshospitalet, Glostrup, and University of Copenhagen, Copenhagen, Denmark
| | - Till Uhlig
- Diakonhjemmet Hospital and University of Oslo, Oslo, Norway
| | - Dan Nordström
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Michael Nurmohamed
- Amsterdam University Medical Centers, Amsterdam, and Amsterdam Rheumatology and Immunology Center, Reade, the Netherlands
| | - Bjorn Gudbjornsson
- Landspitali University Hospital and University of Iceland, Reykjavik, Iceland
| | - Anna Rudin
- Sahlgrenska University Hospital and University of Gothenburg, Gothenburg, Sweden
| | - Mikkel Østergaard
- Copenhagen University Hospital Rigshospitalet, Glostrup, and University of Copenhagen, Copenhagen, Denmark
| | | | | | - Kim Hørslev-Petersen
- University Hospital of Southern Denmark, Sønderborg, and University of Southern Denmark, Odense, Denmark
| | | | - Gerdur Grondal
- Landspitali University Hospital and University of Iceland, Reykjavik, Iceland
| | - Jos W R Twisk
- Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Ronald van Vollenhoven
- Amsterdam University Medical Centers, Amsterdam, the Netherlands, and Karolinska Institute, Stockholm, Sweden
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4
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Brown PM, Anderson AE, Naamane N, Lendrem DW, Morgan AW, Isaacs JD, Pratt AG. Adenosine metabolic signature in circulating CD4+ T cells predicts remission in rheumatoid arthritis. RMD Open 2024; 10:e003858. [PMID: 38367982 PMCID: PMC10875551 DOI: 10.1136/rmdopen-2023-003858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
OBJECTIVES Long-term outcomes in rheumatoid arthritis (RA) depend on early and effective disease control. Methotrexate (MTX) remains the first-line disease modifying therapy, however there are no biomarkers with which to identify those most likely to achieve remission. To address this unmet need we explored metabolic pathways involved in MTX mechanism of action within circulating CD4+T cells in a cohort of treatment naive patients with early RA. METHODS Purified CD4+T cells were isolated from peripheral blood of 68 patients with early RA commencing MTX. The expression of a range of putative MTX metabolism and mechanism of action targets were explored by flow-cytometry and transcriptional analysis. From these data significant predictors of Disease Activity Score 28-C reactive protein (DAS28-CRP) remission (<2.4 at 6 months) were determined by logistic regression (clinical; flow-cytometry data) and linear modelling (gene expression data). RESULTS Low baseline DAS28-CRP was associated with remission at 6 months (p=0.02). Expression of the ectonucleotidase CD39, involved in ATP-ADP conversion during adenosine synthesis, was higher on CD4+CD25 High regulatory T cells at baseline in those achieving remission (molecules of equivalent fluorescence 1264 vs 847; p=0.007). Expression of other adenosine signalling elements in CD4+T cells were also upregulated at baseline in patients achieving remission: AMPD1 (p<0.001), ADORA2b (p=0.039) and ADORA3 (p=0.047). When combined into a single predictive metric, a combination of these variables outperformed baseline DAS28-CRP in prediction of early remission (area under the curve 0.92 vs 0.67, p=0.001) CONCLUSIONS: Adenosine signalling is important in the achievement of early remission with MTX in RA and biomarkers of adenosine activity may hold utility for the stratification of therapy in early disease.
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Affiliation(s)
- Philip M Brown
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- National Institute of Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle Upon Tyne, UK
| | - Amy E Anderson
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- National Institute of Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle Upon Tyne, UK
| | - Najib Naamane
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- National Institute of Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle Upon Tyne, UK
| | - Dennis W Lendrem
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Ann W Morgan
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Biomedical Research Centre and NIHR Leeds Medtech and In Vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - John D Isaacs
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- National Institute of Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle Upon Tyne, UK
| | - Arthur G Pratt
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
- National Institute of Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle Upon Tyne, UK
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5
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Hsieh TY, Lin JF, Liu FC, Chen HC, Lui SW, Chang YT. Functional implications of rs9373441 with FOXP3+Treg and Tr1 for the clinical effectiveness of csDMARDs in rheumatoid arthritis. Clin Chim Acta 2023; 551:117612. [PMID: 37866653 DOI: 10.1016/j.cca.2023.117612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/23/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Rheumatoid arthritis (RA) is characterized by a deficiency in regulatory T cells (Treg), which play a crucial role in immune regulation. While conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) are widely used, there remains a challenge as efficacy varies among patients. In this genome-wide association study (GWAS) involving 410 RA patients, rs9373441 emerged as the most significantly linked single-nucleotide polymorphism (SNP) to csDMARDs response. This non-coding variant functions as a cis-acting regulatory element within the UTRN gene, which is associated with cortical erosion and osteoporosis. Particularly, individuals with the TT allele at rs9373441 exhibited a more favorable response, characterized by a significant increase in FOXP3 + Treg and Type 1 regulatory T cells (Tr1) (p = 0.04, 0.02) and a decrease in Effector T helper cells (Effector Th) (p = 0.03). The GATA3-GCM2-PTH and GATA3-FOXO1-FOXP3 pathways were implicated. RNA-sequencing (RNA-seq) analysis revealed increased expression levels of UTRN, PTH2R, FOXO1, and FOXO3 in good and moderate responders (p = 0.01, 0.03, 0.0005, and 0.02). Notably, the change in FOXP3 + Treg and Tr1 was positively correlated with UTRN expression (both p = 0.03). These findings underscore the critical link between rs9373441 and the response to csDMARDs, empowering clinicians to tailor treatments for enhanced outcomes in patients with RA.
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Affiliation(s)
- Ting-Yu Hsieh
- School of Medicine, National Defense Medical Center, ROC, Taipei, Taiwan
| | - Jun-Fu Lin
- School of Public Health, National Defense Medical Center, ROC, Taipei, Taiwan
| | - Feng-Cheng Liu
- Rheumatology/Immunology and Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, ROC, Taipei, Taiwan
| | - Hsiang-Cheng Chen
- Rheumatology/Immunology and Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, ROC, Taipei, Taiwan
| | - Shan-Wen Lui
- School of Medicine, National Defense Medical Center, ROC, Taipei, Taiwan
| | - Yu-Tien Chang
- School of Public Health, National Defense Medical Center, ROC, Taipei, Taiwan.
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6
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Krainer J, Hendling M, Siebenhandl S, Fuehner S, Kessel C, Verweyen E, Vierlinger K, Foell D, Schönthaler S, Weinhäusel A. Patients with Systemic Juvenile Idiopathic Arthritis (SJIA) Show Differences in Autoantibody Signatures Based on Disease Activity. Biomolecules 2023; 13:1392. [PMID: 37759792 PMCID: PMC10527260 DOI: 10.3390/biom13091392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Systemic juvenile idiopathic arthritis (SJIA) is a severe rheumatic disease in children. It is a subgroup of juvenile idiopathic arthritis (JIA; MIM #604302), which is the most common rheumatic disease in children. The diagnosis of SJIA often comes with a significant delay, and the classification between autoinflammatory and autoimmune disease is still discussed. In this study, we analyzed the immunological responses of patients with SJIA, using human proteome arrays presenting immobilized recombinantly expressed human proteins, to analyze the involvement of autoantibodies in SJIA. Results from group comparisons show several differentially reactive antigens involved in inflammatory processes. Intriguingly, many of the identified antigens had a high reactivity against proteins involved in the NF-κB pathway, and it is also notable that many of the detected DIRAGs are described as dysregulated in rheumatoid arthritis. Our data highlight novel proteins and pathways potentially dysregulated in SJIA and offer a unique approach to unraveling the underlying disease pathogenesis in this chronic arthropathy.
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Affiliation(s)
- Julie Krainer
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Michaela Hendling
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sandra Siebenhandl
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Sabrina Fuehner
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Christoph Kessel
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Emely Verweyen
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Dirk Foell
- Pediatric Rheumatology & Immunology, University Children’s Hospital, 48149 Münster, Germany; (S.F.); (C.K.); (E.V.); (D.F.)
| | - Silvia Schönthaler
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
| | - Andreas Weinhäusel
- Center for Health and Bioresources, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria; (M.H.); (K.V.); (S.S.)
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Wang SS, Lewis MJ, Pitzalis C. DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis. Biomedicines 2023; 11:1987. [PMID: 37509625 PMCID: PMC10377185 DOI: 10.3390/biomedicines11071987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex condition that displays heterogeneity in disease severity and response to standard treatments between patients. Failure rates for conventional, target synthetic, and biologic disease-modifying rheumatic drugs (DMARDs) are significant. Although there are models for predicting patient response, they have limited accuracy, require replication/validation, or for samples to be obtained through a synovial biopsy. Thus, currently, there are no prediction methods approved for routine clinical use. Previous research has shown that genetics and environmental factors alone cannot explain the differences in response between patients. Recent studies have demonstrated that deoxyribonucleic acid (DNA) methylation plays an important role in the pathogenesis and disease progression of RA. Importantly, specific DNA methylation profiles associated with response to conventional, target synthetic, and biologic DMARDs have been found in the blood of RA patients and could potentially function as predictive biomarkers. This review will summarize and evaluate the evidence for DNA methylation signatures in treatment response mainly in blood but also learn from the progress made in the diseased tissue in cancer in comparison to RA and autoimmune diseases. We will discuss the benefits and challenges of using DNA methylation signatures as predictive markers and the potential for future progress in this area.
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Affiliation(s)
- Susan Siyu Wang
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Queen Mary University of London and Barts Health NIHR BRC & NHS Trust, London EC1M 6BQ, UK
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8
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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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9
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Myasoedova E, Athreya AP, Crowson CS, Davis JM, Warrington KJ, Walchak RC, Carlson E, Kalari KR, Bongartz T, Tak PP, van Vollenhoven RF, Padyukov L, Emery P, Morgan A, Wang L, Weinshilboum RM, Matteson EL. Toward Individualized Prediction of Response to Methotrexate in Early Rheumatoid Arthritis: A Pharmacogenomics-Driven Machine Learning Approach. Arthritis Care Res (Hoboken) 2022; 74:879-888. [PMID: 34902228 DOI: 10.1002/acr.24834] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 11/23/2021] [Accepted: 12/07/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To test the ability of machine learning (ML) approaches with clinical and genomic biomarkers to predict methotrexate treatment response in patients with early rheumatoid arthritis (RA). METHODS Demographic, clinical, and genomic data from 643 patients of European ancestry with early RA (mean age 54 years; 70% female) subdivided into a training (n = 336) and validation cohort (n = 307) were used. The genomic data comprised 160 single-nucleotide polymorphisms (SNPs) previously associated with RA or methotrexate metabolism. Response to methotrexate monotherapy was defined as good or moderate by the European Alliance of Associations for Rheumatology (EULAR) response criteria at the 3-month follow-up. Supervised ML methods were trained with 5 repeats and 10-fold cross-validation using the training cohort. Prediction performance was validated in the independent validation cohort. RESULTS Supervised ML methods combining age, sex, smoking, rheumatoid factor, baseline Disease Activity Score in 28 joints (DAS28) scores and 160 SNPs predicted EULAR response at 3 months with the area under the receiver operating curve of 0.84 (P = 0.05) in the training cohort and achieved a prediction accuracy of 76% (P = 0.05) in the validation cohort (sensitivity 72%, specificity 77%). Intergenic SNPs rs12446816, rs13385025, rs113798271, and ATIC (rs2372536) had variable importance above 60.0 and along with baseline DAS28 scores were among the top predictors of methotrexate response. CONCLUSION Pharmacogenomic biomarkers combined with baseline DAS28 scores can be useful in predicting response to methotrexate in patients with early RA. Applying ML to predict treatment response holds promise for guiding effective RA treatment choices, including timely escalation of RA therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Paul P Tak
- Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands, and Candel Therapeutics, Needham, Massachusetts
| | | | - Leonid Padyukov
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Paul Emery
- University of Leeds and NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Ann Morgan
- University of Leeds and NIHR Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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10
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Lim AJW, Lim LJ, Ooi BNS, Koh ET, Tan JWL, Chong SS, Khor CC, Tucker-Kellogg L, Leong KP, Lee CG. Functional coding haplotypes and machine-learning feature elimination identifies predictors of Methotrexate Response in Rheumatoid Arthritis patients. EBioMedicine 2022; 75:103800. [PMID: 35022146 PMCID: PMC8808170 DOI: 10.1016/j.ebiom.2021.103800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Major challenges in large scale genetic association studies include not only the identification of causative single nucleotide polymorphisms (SNPs), but also accounting for SNP-SNP interactions. This study thus proposes a novel feature engineering approach integrating potentially functional coding haplotypes (pfcHap) with machine-learning (ML) feature selection to identify biologically meaningful, possibly causative genetic factors, that take into consideration potential SNP-SNP interactions within the pfcHap, to best predict for methotrexate (MTX) response in rheumatoid arthritis (RA) patients. METHODS Exome sequencing from 349 RA patients were analysed, of which they were split into training and unseen test set. Inferred pfcHaps were combined with 30 non-genetic features to undergo ML recursive feature elimination with cross-validation using the training set. Predictive capacity and robustness of the selected features were assessed using six popular machine learning models through a train set cross-validation and evaluated in an unseen test set. FINDINGS Significantly, 100 features (95 pfcHaps, 5 non-genetic factors) were identified to have good predictive performance (AUC: 0.776-0.828; Sensitivity: 0.656-0.813; Specificity: 0.684-0.868) across all six ML models in an unseen test dataset for the prediction of MTX response in RA patients. INTERPRETATION Majority of the predictive pfcHap SNPs were predicted to be potentially functional and some of the genes in which the pfcHap resides in were identified to be associated with previously reported MTX/RA pathways. FUNDING Singapore Ministry of Health's National Medical Research Council (NMRC) [NMRC/CBRG/0095/2015; CG12Aug17; CGAug16M012; NMRC/CG/017/2013]; National Cancer Center Research Fund and block funding Duke-NUS Medical School.; Singapore Ministry of Education Academic Research Fund Tier 2 grant MOE2019-T2-1-138.
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Affiliation(s)
- Ashley J W Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lee Jin Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Brandon N S Ooi
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Tzun Koh
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
| | - Justina Wei Lynn Tan
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
| | - Samuel S Chong
- Dept of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Lisa Tucker-Kellogg
- Centre for Computational Biology, and Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore; Clinical Research & Innovation Office, Tan Tock Seng Hospital, Singapore.
| | - Caroline G Lee
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Div of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, Singapore; NUS Graduate School, National University of Singapore, Singapore.
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11
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OUP accepted manuscript. Rheumatology (Oxford) 2022; 61:4175-4186. [DOI: 10.1093/rheumatology/keac032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/11/2022] [Indexed: 11/12/2022] Open
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12
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Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Norli ES, Evenrød IM, Andreassen BK, Franzenburg S, Franke A, Rayner S, Gervin K, Lie BA. Methotrexate Treatment of Newly Diagnosed RA Patients Is Associated With DNA Methylation Differences at Genes Relevant for Disease Pathogenesis and Pharmacological Action. Front Immunol 2021; 12:713611. [PMID: 34867944 PMCID: PMC8637827 DOI: 10.3389/fimmu.2021.713611] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022] Open
Abstract
Background Methotrexate (MTX) is the first line treatment of rheumatoid arthritis (RA), and methylation changes in bulk T cells have been reported after treatment with MTX. We have investigated cell-type specific DNA methylation changes across the genome in naïve and memory CD4+ T cells before and after MTX treatment of RA patients. DNA methylation profiles of newly diagnosed RA patients (N=9) were assessed by reduced representation bisulfite sequencing. Results We found that MTX treatment significantly influenced DNA methylation levels at multiple CpG sites in both cell populations. Interestingly, we identified differentially methylated sites annotated to two genes; TRIM15 and SORC2, previously reported to predict treatment outcome in RA patients when measured in bulk T cells. Furthermore, several of the genes, including STAT3, annotated to the significant CpG sites are relevant for RA susceptibility or the action of MTX. Conclusion We detected CpG sites that were associated with MTX treatment in CD4+ naïve and memory T cells isolated from RA patients. Several of these sites overlap genetic regions previously associated with RA risk and MTX treatment outcome.
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Affiliation(s)
- Kari Guderud
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Line H Sunde
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Siri T Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Marthe T Mæhlen
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | | | - Ellen S Norli
- Department of Rheumatology, Martina Hansens Hospital, Bærum, Norway
| | - Ida M Evenrød
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bettina K Andreassen
- Department of Research, Cancer Registry of Norway, Institute for Population-Based Research, Oslo, Norway
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Simon Rayner
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
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Abdel Salam L, Aldarwesh AQ, Eleishi HH. Whole exome sequencing (WES) of methotrexate response/adverse event profile in rheumatoid arthritis patients. THE EGYPTIAN RHEUMATOLOGIST 2021. [DOI: 10.1016/j.ejr.2020.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
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14
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Tsuchiya H, Fujio K. Title Current Status of the Search for Biomarkers for Optimal Therapeutic Drug Selection for Patients with Rheumatoid Arthritis. Int J Mol Sci 2021; 22:ijms22179534. [PMID: 34502442 PMCID: PMC8431405 DOI: 10.3390/ijms22179534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/28/2021] [Accepted: 08/28/2021] [Indexed: 12/19/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive synovitis. It is significantly associated with disability, impaired quality of life, and premature mortality. Recently, the development of biological agents (including tumor necrosis factor-α and interleukin-6 receptor inhibitors) and Janus kinase inhibitors have advanced the treatment of RA; however, it is still difficult to predict which drug will be effective for each patient. To break away from the current therapeutic approaches that could be described as a “lottery,” there is an urgent need to establish biomarkers that stratify patients in terms of expected therapeutic responsiveness. This review deals with recent progress from multi-faceted analyses of the synovial tissue in RA, which is now bringing new insights into diverse features at both the cellular and molecular levels and their potential links with particular clinical phenotypes.
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Artacho A, Isaac S, Nayak R, Flor-Duro A, Alexander M, Koo I, Manasson J, Smith PB, Rosenthal P, Homsi Y, Gulko P, Pons J, Puchades-Carrasco L, Izmirly P, Patterson A, Abramson SB, Pineda-Lucena A, Turnbaugh PJ, Ubeda C, Scher JU. The Pretreatment Gut Microbiome Is Associated With Lack of Response to Methotrexate in New-Onset Rheumatoid Arthritis. Arthritis Rheumatol 2021; 73:931-942. [PMID: 33314800 DOI: 10.1002/art.41622] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/15/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Although oral methotrexate (MTX) remains the anchor drug for rheumatoid arthritis (RA), up to 50% of patients do not achieve a clinically adequate outcome. In addition, there is a lack of prognostic tools for treatment response prior to drug initiation. This study was undertaken to investigate whether interindividual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA. METHODS We performed 16S ribosomal RNA gene and shotgun metagenomic sequencing on the baseline gut microbiomes of drug-naive patients with new-onset RA (n = 26). Results were validated in an additional independent cohort (n = 21). To gain insight into potential microbial mechanisms, we conducted ex vivo experiments coupled with metabolomics analysis to evaluate the association between microbiome-driven MTX depletion and clinical response. RESULTS Our analysis revealed significant associations of the abundance of gut bacterial taxa and their genes with future clinical response (q < 0.05), including orthologs related to purine and MTX metabolism. Machine learning techniques were applied to the metagenomic data, resulting in a microbiome-based model that predicted lack of response to MTX in an independent group of patients. Finally, MTX levels remaining after ex vivo incubation with distal gut samples from pretreatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a possible direct effect of the gut microbiome on MTX metabolism and treatment outcomes. CONCLUSION Taken together, these findings are the first step toward predicting lack of response to oral MTX in patients with new-onset RA and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics.
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Affiliation(s)
| | - Sandrine Isaac
- Center for Public Health Research, FISABIO, Valencia, Spain
| | | | | | | | - Imhoi Koo
- Pennsylvania State University, University Park
| | - Julia Manasson
- New York University School of Medicine and NYU Langone Orthopedic Hospital, New York
| | | | - Pamela Rosenthal
- New York University School of Medicine and NYU Langone Orthopedic Hospital, New York
| | | | - Percio Gulko
- Mount Sinai School of Medicine, New York, New York
| | - Javier Pons
- Center for Public Health Research, FISABIO, Valencia, Spain
| | - Leonor Puchades-Carrasco
- Centro de Investigación Príncipe Felipe and Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Peter Izmirly
- New York University School of Medicine and NYU Langone Orthopedic Hospital, New York
| | | | - Steven B Abramson
- New York University School of Medicine and NYU Langone Orthopedic Hospital, New York
| | - Antonio Pineda-Lucena
- Centro de Investigación Príncipe Felipe and Instituto de Investigación Sanitaria La Fe, Valencia, Spain, and Centro de Investigación Médica Aplicada, Universidad de Navarra, Pamplona, Spain
| | - Peter J Turnbaugh
- University of California and Chan Zuckerberg Biohub, San Francisco, California
| | - Carles Ubeda
- Centro Superior de Investigación en Salud Pública, La Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia, Spain, and CIBERESP, Madrid, Spain
| | - Jose U Scher
- New York University School of Medicine and NYU Langone Orthopedic Hospital, New York
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Dedmon LE. The genetics of rheumatoid arthritis. Rheumatology (Oxford) 2021; 59:2661-2670. [PMID: 32638005 DOI: 10.1093/rheumatology/keaa232] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/03/2020] [Indexed: 12/14/2022] Open
Abstract
RA is a chronic systemic inflammatory disease that primarily affects the small joints of the hands and feet, and results in a mean reduction in life expectancy of 3-10 years. RA is a multigene disorder with a substantial genetic component and a heritability estimate of 60%. Large-scale Genome-Wide Association Studies (GWAS) and meta-analyses have revealed common disease-associated variants in the population that may contribute cumulatively to RA pathogenesis. This review identifies the most significant genetic variants associated with RA susceptibility to date, with particular focus on the contribution of the HLA class II genes across different ethnic groups. Also discussed are the potential applications of pharmacogenomics to RA management by identifying polymorphisms associated with variation in treatment response or toxicity. The use of genetic variants to guide treatment strategy has the potential to not only reduce National Health Service costs, but also drastically improve patient experience and quality of life.
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Lakhanpal A, Smith MH, Donlin LT. Rheumatology in the era of precision medicine: synovial tissue molecular patterns and treatment response in rheumatoid arthritis. Curr Opin Rheumatol 2021; 33:58-63. [PMID: 33229974 DOI: 10.1097/bor.0000000000000767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW A critical unmet need in rheumatoid arthritis (RA) is the identification of biomarkers that predict which of the available medications will be most effective for an individual in order to lower disease activity sooner than is afforded by the current treat-to-target approach. Here we will discuss recent reports examining the potential for synovial tissue molecular, cellular, and spatial profiling in defining objective measures of treatment response and therein developing personalized medicine for RA. RECENT FINDINGS Recent high-dimensional molecular profiling of RA synovium has provided unprecedented resolution of the cell types and pathways in tissues affected by rheumatic diseases. Heightened attention to tissue architecture is also emerging as a means to classify individual disease variation that may allow patients to be further stratified by therapeutic response. Although this wealth of data may have already pinpointed promising biomarkers, additional studies, likely including tissue-based functional drug response assays, will be required to demonstrate how the complex tissue environment responds. SUMMARY Molecular, cellular, and more recently spatial profiling of the RA synovium are uncovering fundamental features of the disease. Current investigations are examining whether this information will provide meaningful biomarkers for individualized medicine in RA.
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Affiliation(s)
| | | | - Laura T Donlin
- Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery
- Weill Cornell Medical College and Graduate School, New York, New York, USA
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Biomarkers to Personalize the Treatment of Rheumatoid Arthritis: Focus on Autoantibodies and Pharmacogenetics. Biomolecules 2020; 10:biom10121672. [PMID: 33327600 PMCID: PMC7765045 DOI: 10.3390/biom10121672] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 12/19/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease that is very complex and heterogeneous. If not adequately treated, RA patients are likely to manifest excess of morbidity and disability with an important impact on the quality of life. Pharmacological treatment is based on the administration of the disease-modifying antirheumatic drugs (DMARDs), subdivided into conventional synthetic (csDMARDs), targeted synthetic (tsDMARDs), and biological (bDMARDs). bDMARDs are now frequently administered in patients, both as alternative treatment and together with csDMARDs. Unfortunately, there is a therapeutic response variability both to old and new drugs. Therefore, to identify pre-therapeutic and on-treatment predictors of response is a priority. This review aims to summarize recent advances in understanding the causes of the variability in treatment response in RA, with particular attention to predictive potential of autoantibodies and DMARD pharmacogenetics. In recent years, several biomarkers have been proposed to personalize the therapy. Unfortunately, a magic bullet does not exist, as many factors concur to disease susceptibility and treatment outcomes, acting around the patient’s congenital background. Models integrating demographic, clinical, biochemical, and genetic data are needed to enhance the predictive capacity of specific factors singularly considered to optimize RA treatment in light of multidisciplinary patient management.
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Gosselt HR, Verhoeven MMA, de Rotte MCFJ, Pluijm SMF, Muller IB, Jansen G, Tekstra J, Bulatović-Ćalasan M, Heil SG, Lafeber FPJG, Hazes JMW, de Jonge R. Validation of a Prognostic Multivariable Prediction Model for Insufficient Clinical Response to Methotrexate in Early Rheumatoid Arthritis and Its Clinical Application in Evidencio. Rheumatol Ther 2020; 7:837-850. [PMID: 32926395 PMCID: PMC7695780 DOI: 10.1007/s40744-020-00230-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Methotrexate (MTX) constitutes the first-line therapy in rheumatoid arthritis (RA), yet approximately 30% of the patients do not benefit from MTX. Recently, we reported a prognostic multivariable prediction model for insufficient clinical response to MTX at 3 months of treatment in the treatment in the Rotterdam Early Arthritis Cohort (tREACH), including baseline predictors: Disease activity score 28 (DAS28), Health Assessment Questionnaire (HAQ), erythrocyte folate, single-nucleotide polymorphisms (SNPs; ABCB1, ABCC3), smoking, and BMI. The purpose of the current study was (1) to externally validate the model and (2) to enhance the model's clinical applicability. METHODS Erythrocyte folate and SNPs were assessed in 91 early disease-modifying antirheumatic drug (DMARD)-naïve RA patients starting MTX in the external validation cohort (U-Act-Early). Insufficient response (DAS28 > 3.2) was determined after 3 months and non-response after 6 months of therapy. The previously developed prediction model was considered successfully validated in the U-Act-Early (validation cohort) if the area under the curve (AUC) of the receiver operating characteristic (ROC) was not significantly lower than in the tREACH (derivation cohort). RESULTS The AUCs in U-Act-Early at three and 6 months were 0.75 (95% CI 0.64-0.85) and 0.71 (95% CI 0.60-0.82) respectively, similar to the tREACH. Baseline DAS28 > 5.1 and HAQ > 0.6 were the strongest predictors. The model was simplified by excluding the SNPs, while still classifying 73% correctly. Furthermore, interaction terms between BMI and HAQ and BMI and erythrocyte folate significantly improved the model increasing correct classification to 75%. Results were successfully implemented in Evidencio online platform assisting clinicians in shared decision-making to intensify treatment when appropriate. CONCLUSIONS We successfully externally validated our recently reported prediction model for MTX non-response and enhanced its clinical application thus enabling its evaluation in a clinical trial. TRIAL REGISTRATION The U-Act-Early is registered at ClinicalTrials.gov. number: NCT01034137. tREACH is registered retrospectively at ISRCTN registry, number: ISRCTN26791028 at 23 August 2007.
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Affiliation(s)
- Helen R Gosselt
- Amsterdam Gastroenterology and Metabolism, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Maxime M A Verhoeven
- Department of Rheumatology and Clinical Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Maurits C F J de Rotte
- Amsterdam Gastroenterology and Metabolism, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Gastroenterology and Metabolism, Department of Clinical Chemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Saskia M F Pluijm
- Department of Paediatric Oncology, Prinses Máxima Centre for Paediatric Oncology, Utrecht, The Netherlands
| | - Ittai B Muller
- Amsterdam Gastroenterology and Metabolism, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerrit Jansen
- Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Janneke Tekstra
- Department of Rheumatology and Clinical Immunology, UMC Utrecht, Utrecht, The Netherlands
| | | | - Sandra G Heil
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Floris P J G Lafeber
- Department of Rheumatology and Clinical Immunology, UMC Utrecht, Utrecht, The Netherlands
| | - Johanna M W Hazes
- Department of Rheumatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert de Jonge
- Amsterdam Gastroenterology and Metabolism, Department of Clinical Chemistry, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Burren OS, Reales G, Wong L, Bowes J, Lee JC, Barton A, Lyons PA, Smith KGC, Thomson W, Kirk PDW, Wallace C. Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases. Genome Med 2020; 12:106. [PMID: 33239102 PMCID: PMC7687775 DOI: 10.1186/s13073-020-00797-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified pervasive sharing of genetic architectures across multiple immune-mediated diseases (IMD). By learning the genetic basis of IMD risk from common diseases, this sharing can be exploited to enable analysis of less frequent IMD where, due to limited sample size, traditional GWAS techniques are challenging. METHODS Exploiting ideas from Bayesian genetic fine-mapping, we developed a disease-focused shrinkage approach to allow us to distill genetic risk components from GWAS summary statistics for a set of related diseases. We applied this technique to 13 larger GWAS of common IMD, deriving a reduced dimension "basis" that summarised the multidimensional components of genetic risk. We used independent datasets including the UK Biobank to assess the performance of the basis and characterise individual axes. Finally, we projected summary GWAS data for smaller IMD studies, with less than 1000 cases, to assess whether the approach was able to provide additional insights into genetic architecture of less common IMD or IMD subtypes, where cohort collection is challenging. RESULTS We identified 13 IMD genetic risk components. The projection of independent UK Biobank data demonstrated the IMD specificity and accuracy of the basis even for traits with very limited case-size (e.g. vitiligo, 150 cases). Projection of additional IMD-relevant studies allowed us to add biological interpretation to specific components, e.g. related to raised eosinophil counts in blood and serum concentration of the chemokine CXCL10 (IP-10). On application to 22 rare IMD and IMD subtypes, we were able to not only highlight subtype-discriminating axes (e.g. for juvenile idiopathic arthritis) but also suggest eight novel genetic associations. CONCLUSIONS Requiring only summary-level data, our unsupervised approach allows the genetic architectures across any range of clinically related traits to be characterised in fewer dimensions. This facilitates the analysis of studies with modest sample size by matching shared axes of both genetic and biological risk across a wider disease domain, and provides an evidence base for possible therapeutic repurposing opportunities.
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Affiliation(s)
- Oliver S Burren
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Guillermo Reales
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Limy Wong
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - John Bowes
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - James C Lee
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Anne Barton
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Wendy Thomson
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Paul D W Kirk
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK
- Cancer Research UK Cambridge Centre, Ovarian Cancer Programme, University of Cambridge Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Chris Wallace
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- MRC Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge, CB2 0SR, UK.
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Bao Q, Zhang L, Wang N, Gabet B, Yang W, Gao X, You Q, Jiang Z. Hydrogen Peroxide Inducible JAK3 Covalent Inhibitor: Prodrug for the Treatment of RA with Enhanced Safety Profile. ACS Med Chem Lett 2020; 11:2182-2189. [PMID: 33214827 DOI: 10.1021/acsmedchemlett.0c00323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Selective inhibition of Janus kinases (JAKs) is an arising strategy in drug discovery. Covalent inhibitors targeting a unique cysteine in JAK3 exhibit ultraselectivity among JAK family members. However, safety and tissue specific concerns still remain. A prodrug of a known JAK3 covalent inhibitor sensitive to H2O2 was designed and synthesized and its therapeutic effect was evaluated in the CIA (collagen-induced arthritis) mice model of RA (rheumatoid arthritis). The prodrug strategy relied on the introduction of a hydrogen peroxide-sensitive borate trigger group to avoid random covalent binding to thiol functionalities in biomacromolecules. The results show that the prodrug can be activated and released under pathophysiological concentration of H2O2. In addition, the prodrug demonstrated stability to the physiological environment. In comparison to the parent compound, the prodrug showed a similar therapeutic effect in the CIA model but notably exhibited lower toxicity and a larger therapeutic window.
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Affiliation(s)
- Qichao Bao
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Liangying Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Nan Wang
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Brian Gabet
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware Street, SE, Minneapolis, Minnesota 55414, United States
| | - Weikang Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xingyang Gao
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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22
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Ling SF, Bluett J. Pharmacogenetics of methotrexate response in rheumatoid arthritis: an update. Pharmacogenomics 2020; 21:3-6. [PMID: 31849277 DOI: 10.2217/pgs-2019-0154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Stephanie F Ling
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, Oxford Road, Manchester, M13 9PT, UK.,The Nowgen Centre, 29 Grafton Street, Mancheser, M13 9WL, UK
| | - James Bluett
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, Oxford Road, Manchester, M13 9PT, UK.,The Nowgen Centre, 29 Grafton Street, Mancheser, M13 9WL, UK
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23
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New era for outcomes and management of rheumatoid arthritis: Facing the individualized treatment challenge. Joint Bone Spine 2020; 88:105066. [PMID: 32952004 DOI: 10.1016/j.jbspin.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/26/2020] [Indexed: 11/23/2022]
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24
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Szostak B, Machaj F, Rosik J, Pawlik A. Using pharmacogenetics to predict methotrexate response in rheumatoid arthritis patients. Expert Opin Drug Metab Toxicol 2020; 16:617-626. [DOI: 10.1080/17425255.2020.1777279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bartosz Szostak
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Filip Machaj
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Jakub Rosik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
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25
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Esperon P, Giletti A. Genetic markers that could influence clinical decision making during treatment with methotrexate. Pharmacogenomics 2020; 21:505-507. [DOI: 10.2217/pgs-2019-0188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Patricia Esperon
- Molecular Genetics Laboratory, Clinical Biochemistry Department, School of Chemistry, Universidad de la República, Montevideo, 11200, Uruguay
| | - Andrea Giletti
- Molecular Genetics Laboratory, Clinical Biochemistry Department, School of Chemistry, Universidad de la República, Montevideo, 11200, Uruguay
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26
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Plant D, Barton A. Adding value to real-world data: the role of biomarkers. Rheumatology (Oxford) 2020; 59:31-38. [PMID: 31329972 PMCID: PMC6909909 DOI: 10.1093/rheumatology/kez113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/28/2019] [Indexed: 12/13/2022] Open
Abstract
Adding biomarker information to real world datasets (e.g. biomarker data collected into disease/drug registries) can enhance mechanistic understanding of intra-patient differences in disease trajectories and differences in important clinical outcomes. Biomarkers can detect pathologies present early in disease potentially paving the way for preventative intervention strategies, which may help patients to avoid disability, poor treatment outcome, disease sequelae and premature mortality. However, adding biomarker data to real world datasets comes with a number of important challenges including sample collection and storage, study design and data analysis and interpretation. In this narrative review we will consider the benefits and challenges of adding biomarker data to real world datasets and discuss how biomarker data have added to our understanding of complex diseases, focusing on rheumatoid arthritis.
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Affiliation(s)
- Darren Plant
- Manchester Academic Health Science Centre, The University of Manchester, Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, UK.,Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anne Barton
- Manchester Academic Health Science Centre, The University of Manchester, Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, UK.,Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
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27
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Feng X, Hao X, Shi R, Xia Z, Huang L, Yu Q, Zhou F. Detection and Comparative Analysis of Methylomic Biomarkers of Rheumatoid Arthritis. Front Genet 2020; 11:238. [PMID: 32292416 PMCID: PMC7119472 DOI: 10.3389/fgene.2020.00238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disorder influenced by both genetic and environmental factors. To investigate possible contributions of DNA methylation to the etiology of RA with minimum confounding genetic heterogeneity, we investigated genome-wide DNA methylation in disease-discordant monozygotic twin pairs. This study hypothesized that methylomic biomarkers might facilitate accurate RA detection. A comprehensive series of biomarker detection algorithms were utilized to find the best methylomic biomarkers for detecting RA patients using the methylomic data of the peripheral blood samples. The best model achieved 100.00% in accuracy (Acc) with 81 methylomic biomarkers and a 10-fold cross-validation (10FCV) strategy. Some of the methylomic biomarkers were experimentally confirmed to be associated with the onset or development of RA. It is also interesting to observe that many of the detected biomarkers were from chromosome Y, supporting the knowledge that RA has a significant gender discrepancy.
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Affiliation(s)
- Xin Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China.,Jilin Institute of Chemical Technology, Jilin, China.,BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Xubing Hao
- BioKnow Health Informatics Lab, College of Software, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Sciences, Jilin University, Changchun, China
| | - Zhiqiang Xia
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Fengfeng Zhou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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28
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Methotrexate and its mechanisms of action in inflammatory arthritis. Nat Rev Rheumatol 2020; 16:145-154. [PMID: 32066940 DOI: 10.1038/s41584-020-0373-9] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 11/08/2022]
Abstract
Despite the introduction of numerous biologic agents for the treatment of rheumatoid arthritis (RA) and other forms of inflammatory arthritis, low-dose methotrexate therapy remains the gold standard in RA therapy. Methotrexate is generally the first-line drug for the treatment of RA, psoriatic arthritis and other forms of inflammatory arthritis, and it enhances the effect of most biologic agents in RA. Understanding the mechanism of action of methotrexate could be instructive in the appropriate use of the drug and in the design of new regimens for the treatment of RA. Although methotrexate is one of the first examples of intelligent drug design, multiple mechanisms potentially contribute to the anti-inflammatory actions of methotrexate, including the inhibition of purine and pyrimidine synthesis, transmethylation reactions, translocation of nuclear factor-κB (NF-κB) to the nucleus, signalling via the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway and nitric oxide production, as well as the promotion of adenosine release and expression of certain long non-coding RNAs.
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29
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Rheumatological manifestations in inborn errors of immunity. Pediatr Res 2020; 87:293-299. [PMID: 31581173 DOI: 10.1038/s41390-019-0600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 11/08/2022]
Abstract
Rare monogenetic diseases serve as natural models to dissect the molecular pathophysiology of the complex disease traits. Rheumatologic disorders by their nature are considered complex diseases with partially genetic origin, as illustrated by their heterogeneous genetic background and variable phenotypic presentation. Recent advances in genetic technologies have helped uncover multiple variants associated with disease susceptibility; however, a precise understanding of genotype-phenotype relationships is still missing. Inborn errors of immunity (IEIs), in addition to recurrent infections, may also present with autoimmune and autoinflammatory rheumatologic manifestations and have provided insights for understanding the underlying the principles of immune system homeostasis and mechanisms of immune dysregulation. This review discusses the rheumatologic manifestations in IEIs with overlapping and differentiating features in immunodeficiencies and rheumatologic disorders.
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30
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Jekic B, Maksimovic N, Damnjanovic T. Methotrexate pharmacogenetics in the treatment of rheumatoid arthritis. Pharmacogenomics 2019; 20:1235-1245. [DOI: 10.2217/pgs-2019-0121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For many decades, methotrexate (MXT) has remained the drug of choice in the treatment of rheumatoid arthritis (RA). Unfortunately, a considerable number of patients do not achieve an appropriate therapeutic response. Pharmacogenetics studies do not give usable results regarding differences in MTX response among RA patients. The mechanism of MTX action in RA is not completely understood. We present and discuss data regarding the molecular basis of folate and adenosine pathways, the most obvious MTX targets, to explain possible causes of therapy failure. The molecular basis of the disease could also have an impact on therapy outcomes and in this review we explore this. Finally, we make a short review of available pharmacogenetics study results.
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Affiliation(s)
- Biljana Jekic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade,11000 Belgrade, Serbia
| | - Nela Maksimovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade,11000 Belgrade, Serbia
| | - Tatjana Damnjanovic
- Institute of Human Genetics, Faculty of Medicine, University of Belgrade,11000 Belgrade, Serbia
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31
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Bedoui Y, Guillot X, Sélambarom J, Guiraud P, Giry C, Jaffar-Bandjee MC, Ralandison S, Gasque P. Methotrexate an Old Drug with New Tricks. Int J Mol Sci 2019; 20:ijms20205023. [PMID: 31658782 PMCID: PMC6834162 DOI: 10.3390/ijms20205023] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/16/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
Methotrexate (MTX) is the first line drug for the treatment of a number of rheumatic and non-rheumatic disorders. It is currently used as an anchor disease, modifying anti-rheumatic drug in the treatment of rheumatoid arthritis (RA). Despite the development of numerous new targeted therapies, MTX remains the backbone of RA therapy due to its potent efficacy and tolerability. There has been also a growing interest in the use of MTX in the treatment of chronic viral mediated arthritis. Many viruses—including old world alphaviruses, Parvovirus B19, hepatitis B/C virus, and human immunodeficiency virus—have been associated with arthritogenic diseases and reminiscent of RA. MTX may provide benefits although with the potential risk of attenuating patients’ immune surveillance capacities. In this review, we describe the emerging mechanisms of action of MTX as an anti-inflammatory drug and complementing its well-established immunomodulatory activity. The mechanisms involve adenosine signaling modulation, alteration of cytokine networks, generation of reactive oxygen species and HMGB1 alarmin suppression. We also provide a comprehensive understanding of the mechanisms of MTX toxic effects. Lastly, we discussed the efficacy, as well as the safety, of MTX used in the management of viral-related rheumatic syndromes.
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Affiliation(s)
- Yosra Bedoui
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM U1187, CNRS 9192, IRD 249, Université de La Réunion-Plateforme Technologique CYROI-2, rue Maxime Rivière, 97490 Sainte-Clotilde, France.
| | - Xavier Guillot
- Service de Rhumatologie, CHU La Réunion site Félix Guyon, Allée des Topazes, CS11021, 97400 Saint Denis de La Réunion, France.
| | - Jimmy Sélambarom
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM U1187, CNRS 9192, IRD 249, Université de La Réunion-Plateforme Technologique CYROI-2, rue Maxime Rivière, 97490 Sainte-Clotilde, France.
| | - Pascale Guiraud
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM U1187, CNRS 9192, IRD 249, Université de La Réunion-Plateforme Technologique CYROI-2, rue Maxime Rivière, 97490 Sainte-Clotilde, France.
| | - Claude Giry
- Laboratoire de biologie, CNR associé des arbovirus, CHU La Réunion site Félix Guyon, Allée des Topazes, CS11021, 97400 Saint Denis de La Réunion, France.
| | - Marie Christine Jaffar-Bandjee
- Laboratoire de biologie, CNR associé des arbovirus, CHU La Réunion site Félix Guyon, Allée des Topazes, CS11021, 97400 Saint Denis de La Réunion, France.
| | - Stéphane Ralandison
- Service de Rhumatologie-Médecine Interne, CHU Morafeno, Route d'Ivoloina 501, Toamasina, Madagascar.
| | - Philippe Gasque
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM U1187, CNRS 9192, IRD 249, Université de La Réunion-Plateforme Technologique CYROI-2, rue Maxime Rivière, 97490 Sainte-Clotilde, France.
- Pôle de Biologie, secteur Laboratoire d'Immunologie Clinique et Expérimentale de la zone de l'Océan Indien (LICE-OI), CHU La Réunion site Félix Guyon, Allée des Topazes, CS11021, 97400 Saint Denis de La Réunion, France.
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32
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Takahashi K, Nakamura H, Watanabe A, Majima T, Koiwa M, Kamada T, Takai S. Polymorphism in Organic Anion-Transporting Polypeptide Gene Related to Methotrexate Response in Rheumatoid Arthritis Treatment. J NIPPON MED SCH 2019; 86:149-158. [PMID: 31292326 DOI: 10.1272/jnms.jnms.2019_86-303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Methotrexate (MTX) is still the first-choice drug for the treatment of rheumatoid arthritis (RA). In Japan, MTX doses of up to 16 mg/week were approved in 2011. In this study, we aimed to identify the gene polymorphisms that can predict therapeutic effects of MTX in Japanese patients in current clinical settings. METHODS This study involved 171 patients with RA (all Japanese nationals, age 63.5±10.0 years) who had been administered MTX. The analyzed polymorphisms included 82 single nucleotide polymorphisms (SNPs) involved in the MTX pharmacological pathway or in the pathogenesis of RA. Responders were patients who showed high sustained remission or low disease activity with MTX or conventional disease-modifying anti-rheumatic drugs (DMARDs) treatment beyond 6 months. Non-responders were patients who showed moderate or high disease activity, who were prescribed biological DMARDs. A logistic model was constructed with Responder/Non-responder as the target variable, and minor allele frequency was set as an explanatory variable. RESULTS None of the 82 SNPs targeted for analysis met the Bonferroni significance threshold of 6.098×10-4. However, we identified SLCO1B1 rs11045879 as an SNP that might yield significant results if the number of patients were to be increased (P=0.015). CONCLUSIONS The rs11045879 minor allele in the SLCO1B1 gene is a potential predictor of non-responders to MTX treatment among Japanese RA patients. In future collaborative research, we will investigate whether the association with SLCO1B1 polymorphism is significant by performing statistical analysis with a larger study population.
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Affiliation(s)
- Kenji Takahashi
- Department of Orthopaedic Surgery, International University of Health and Welfare Hospital
| | | | - Atsushi Watanabe
- Division of Personalized Genetic Medicine, Nippon Medical School Hospital
| | | | - Masahito Koiwa
- Department of Orthopaedic Surgery, Shuwa General Hospital
| | | | - Shinro Takai
- Department of Orthopaedic Surgery, Nippon Medical School
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33
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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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34
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He X, Sun M, Liang S, Li M, Li L, Yang Y. Association between ABCB1 C3435T polymorphism and methotrexate treatment outcomes in rheumatoid arthritis patients: a meta-analysis. Pharmacogenomics 2019; 20:381-392. [PMID: 30983549 DOI: 10.2217/pgs-2018-0172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: This study was conducted to investigate the relationship between ABCB1 gene C3435T polymorphism and methotrexate treatment outcomes in rheumatoid arthritis patients. Methods: Seven electronic databases (PubMed, EMBASE, Web of Science, Cochrane, OVID, Chinese biomedical literature [CBM], China National Knowledge Infrastructure [CNKI] and Wanfang databases) were searched to select eligible publications until 18 July 2018. The references of relevant articles were also manually searched. The quality evaluation of the included studies was carried out according to the guidelines of the Newcastle–Ottawa Scale. Data were analyzed with Review Manager 5.3 and Stata 13.0 software. In total, 12 articles involving 2014 patients were included. Conclusion: Our results demonstrated that the ABCB1 gene C3435T polymorphism might be a reliable predictor of response to methotrexate in rheumatoid arthritis patients. However, well-designed, multicenter and large-scale prospective studies are required to further confirm the validity of our results.
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Affiliation(s)
- Xiao He
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
- First Department, State Key Laboratory of Trauma, Burn & Combined Injury, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
| | - Mingfang Sun
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
| | - Shenju Liang
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
| | - Mengshan Li
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
| | - Liangliang Li
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
| | - Yi Yang
- Department of Rheumatology & Clinical Immunology, Daping Hospital & Research Institute of Surgery, Army Medical University, Chongqing 400042, PR China
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35
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Barrett JH. Genome-wide association studies of therapeutic response: addressing the complexities. Pharmacogenomics 2019; 20:213-216. [PMID: 30767725 DOI: 10.2217/pgs-2018-0204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Jennifer H Barrett
- Leeds Institute for Data Analytics, School of Medicine, University of Leeds, Leeds, UK
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36
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Dai C, Kuo SJ, Hu SL, Tsai CH, Huang YL, Huang CC, Wang L, Xu G, Su CM, Tang CH. VEGF-C Gene Polymorphisms Increase Susceptibility to Rheumatoid Arthritis. Int J Med Sci 2019; 16:1397-1403. [PMID: 31692815 PMCID: PMC6818187 DOI: 10.7150/ijms.34659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
Vascular endothelial growth factor C (VEGF-C) promotes angiogenesis, a prominent feature in rheumatoid synovitis, contributing to the perpetuation of the global burden of rheumatoid arthritis (RA). VEGF-C gene polymorphisms predict the risk of developing various human diseases, such as urothelial cell carcinoma, oral cancer and coronary artery disease. We sought to determine whether single nucleotide polymorphisms (SNPs) of the VEGF-C gene can predict the risk of RA. Our study recruited 210 patients with RA and 373 healthy controls between 2007 and 2015, and performed comparative genotyping for SNPs rs7664413, rs11947611, rs1485766, rs2046463 and rs3775194. In analyses adjusted for potential covariates, we found that compared with subjects with the A/A genotype of SNP rs11947611, those with the A/G genotype were 40% more likely to develop RA (adjusted odds ratio [AOR] 0.61; 95% confidence interval [CI] 0.40 to 0.92; p = 0.02). In addition, subjects lacking the A/A genotype (A/G, G/G) of SNP rs2046463 were more than twice as likely as those with the A/A genotype to require methotrexate (AOR 2.23, 95% CI 1.25 to 3.98; p = 0.01), while those who lacked the G/G genotype (G/C, C/C) in the SNP rs3775194 had a significantly lower risk of requiring prednisolone as compared with those with the G/G genotype (AOR 0.39, 95% CI 0.19 to 0.79; p = 0.01). Our findings suggest that VEGF-C gene polymorphisms might serve as a diagnostic marker and therapeutic target for RA therapy. Pharmacotherapies that modulate the activity of the VEGF-C gene may be promising for RA treatment.
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Affiliation(s)
- Chengqian Dai
- Department of Orthopedics, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Shu-Jui Kuo
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Sung-Lin Hu
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Family Medicine, China Medical University Hsinchu Hospital, Hsinchu, Taiwan
| | - Chun-Hao Tsai
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Orthopedic Surgery, China Medical University Hospital, Taichung, Taiwan
| | - Yuan-Li Huang
- Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan
| | - Chien-Chung Huang
- School of Medicine, China Medical University, Taichung, Taiwan.,Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Lihong Wang
- Department of Orthopedics, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Guohong Xu
- Department of Orthopedics, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Chen-Ming Su
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Chih-Hsin Tang
- School of Medicine, China Medical University, Taichung, Taiwan.,Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan.,Chinese Medicine Research Center, China Medical University, Taichung, Taiwan
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37
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Cherlin S, Plant D, Taylor JC, Colombo M, Spiliopoulou A, Tzanis E, Morgan AW, Barnes MR, McKeigue P, Barrett JH, Pitzalis C, Barton A, Consortium MATURA, Cordell HJ. Prediction of treatment response in rheumatoid arthritis patients using genome-wide SNP data. Genet Epidemiol 2018; 42:754-771. [PMID: 30311271 PMCID: PMC6334178 DOI: 10.1002/gepi.22159] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/06/2018] [Accepted: 07/28/2018] [Indexed: 01/13/2023]
Abstract
Although a number of treatments are available for rheumatoid arthritis (RA), each of them shows a significant nonresponse rate in patients. Therefore, predicting a priori the likelihood of treatment response would be of great patient benefit. Here, we conducted a comparison of a variety of statistical methods for predicting three measures of treatment response, between baseline and 3 or 6 months, using genome-wide SNP data from RA patients available from the MAximising Therapeutic Utility in Rheumatoid Arthritis (MATURA) consortium. Two different treatments and 11 different statistical methods were evaluated. We used 10-fold cross validation to assess predictive performance, with nested 10-fold cross validation used to tune the model hyperparameters when required. Overall, we found that SNPs added very little prediction information to that obtained using clinical characteristics only, such as baseline trait value. This observation can be explained by the lack of strong genetic effects and the relatively small sample sizes available; in analysis of simulated and real data, with larger effects and/or larger sample sizes, prediction performance was much improved. Overall, methods that were consistent with the genetic architecture of the trait were able to achieve better predictive ability than methods that were not. For treatment response in RA, methods that assumed a complex underlying genetic architecture achieved slightly better prediction performance than methods that assumed a simplified genetic architecture.
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Affiliation(s)
- Svetlana Cherlin
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Darren Plant
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
| | - John C. Taylor
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
- NIHR Leeds Biomedical Research CentreLeeds Teaching Hospitals NHS TrustLeedsUK
| | - Marco Colombo
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
| | - Athina Spiliopoulou
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
| | - Evan Tzanis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryQueen Mary University of London and Barts Health NHS TrustLondonUK
| | - Ann W. Morgan
- NIHR Leeds Biomedical Research CentreLeeds Teaching Hospitals NHS TrustLeedsUK
- Leeds Institute of Rheumatic and Musculoskeletal MedicineUniversity of LeedsLeedsUK
| | - Michael R. Barnes
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryQueen Mary University of London and Barts Health NHS TrustLondonUK
| | - Paul McKeigue
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
| | - Jennifer H. Barrett
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
- NIHR Leeds Biomedical Research CentreLeeds Teaching Hospitals NHS TrustLeedsUK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryQueen Mary University of London and Barts Health NHS TrustLondonUK
| | - Anne Barton
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal ResearchThe University of ManchesterManchesterUK
| | - MATURA Consortium
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
- NIHR Leeds Biomedical Research CentreLeeds Teaching Hospitals NHS TrustLeedsUK
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and InformaticsUniversity of EdinburghEdinburghUK
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and the London School of Medicine and DentistryQueen Mary University of London and Barts Health NHS TrustLondonUK
- Leeds Institute of Rheumatic and Musculoskeletal MedicineUniversity of LeedsLeedsUK
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal ResearchThe University of ManchesterManchesterUK
| | - Heather J. Cordell
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation TrustManchester Academic Health Science CentreManchesterUK
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38
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Sumitomo S, Nagafuchi Y, Tsuchida Y, Tsuchiya H, Ota M, Ishigaki K, Suzuki A, Kochi Y, Fujio K, Yamamoto K. Transcriptome analysis of peripheral blood from patients with rheumatoid arthritis: a systematic review. Inflamm Regen 2018; 38:21. [PMID: 30410636 PMCID: PMC6217768 DOI: 10.1186/s41232-018-0078-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022] Open
Abstract
In the era of precision medicine, transcriptome analysis of whole gene expression is an essential technology. While DNA microarray has a limited dynamic range and a problem of background hybridization, RNA sequencing (RNA-seq) has a broader dynamic range and a lower background signal that increase the sensitivity and reproducibility. While transcriptome analyses in rheumatoid arthritis (RA) have generally focused on whole peripheral blood mononuclear cells (PBMC), analyses of detailed cell subsets have an increased need for understanding the pathophysiology of disease because the involvement of CD4+ T cells in the pathogenesis of RA has been established. Transcriptome analysis of detailed CD4+ T cell subsets or neutrophils shed new light on the pathophysiology of RA. There are several analyses about the effect of biological treatment. Many studies report the association between type I interferon signature gene expression and response to therapy.
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Affiliation(s)
- Shuji Sumitomo
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yasuo Nagafuchi
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Yumi Tsuchida
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Haruka Tsuchiya
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Mineto Ota
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuyoshi Ishigaki
- 2Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Akari Suzuki
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Yuta Kochi
- 3Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
| | - Keishi Fujio
- 1Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655 Japan
| | - Kazuhiko Yamamoto
- 4Center for Integrative Medical Sciences, the Institute of Physical and Chemical Research (RIKEN), 1-7-22 Suehirocho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045 Japan
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