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Sharma SD, Leung SH, Viatte S. Genetics of rheumatoid arthritis. Best Pract Res Clin Rheumatol 2024:101968. [PMID: 38955657 DOI: 10.1016/j.berh.2024.101968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
In the past four decades, a plethora of genetic association studies have been carried out in cohorts of patients with rheumatoid arthritis. These studies have highlighted key aspects of disease pathogenesis and suggested causal mechanisms. In this review, we discuss major advances in our understanding of the genetic architecture of rheumatoid arthritis susceptibility, severity and treatment response and explain how genetics supports current models of disease pathogenesis and outcome. We outline future research directions, like Mendelian randomisation, and present a number of potential avenues for clinical translation, including risk and outcome prediction, patient stratification into treatment response groups and pharmacological applications.
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Affiliation(s)
- Seema D Sharma
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK; NIHR Manchester Musculoskeletal Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Shek H Leung
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Sebastien Viatte
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK; NIHR Manchester Musculoskeletal Biomedical Research Centre, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
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2
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Bo L, Jin X, Hu Y, Yang R. Role of Liquid Biopsies in Rheumatoid Arthritis. Methods Mol Biol 2023; 2695:237-246. [PMID: 37450123 DOI: 10.1007/978-1-0716-3346-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease caused by genetic and environmental factors. Early diagnosis is crucial for effective therapy and prognosis of RA, while biomarkers play important roles in early diagnosis. Traditional laboratory tests include rheumatoid factor, anti-cyclic citrullinated peptide antibody, which are inadequate in the ability of early diagnosis. Liquid biopsy technology is a technique using biomarkers found in the blood, urine, and other biological samples from patients, including DNA, RNA, exosome, etc. Evidence indicates that these biomarkers are involved in pathological and physiological conditions of RA. We reviewed the effects of liquid biopsy technology in the early diagnosis of RA and may provide new ideas for effective and precise treatment.
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Affiliation(s)
- Lin Bo
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaojia Jin
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yaqi Hu
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Ru Yang
- Department of Rheumatology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Roodenrijs NMT, Welsing PMJ, van Roon J, Schoneveld JLM, van der Goes MC, Nagy G, Townsend MJ, van Laar JM. Mechanisms underlying DMARD inefficacy in difficult-to-treat rheumatoid arthritis: a narrative review with systematic literature search. Rheumatology (Oxford) 2022; 61:3552-3566. [PMID: 35238332 PMCID: PMC9434144 DOI: 10.1093/rheumatology/keac114] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 12/03/2022] Open
Abstract
Management of RA patients has significantly improved over the past decades. However, a substantial proportion of patients is difficult-to-treat (D2T), remaining symptomatic after failing biological and/or targeted synthetic DMARDs. Multiple factors can contribute to D2T RA, including treatment non-adherence, comorbidities and co-existing mimicking diseases (e.g. fibromyalgia). Additionally, currently available biological and/or targeted synthetic DMARDs may be truly ineffective ('true' refractory RA) and/or lead to unacceptable side effects. In this narrative review based on a systematic literature search, an overview of underlying (immune) mechanisms is presented. Potential scenarios are discussed including the influence of different levels of gene expression and clinical characteristics. Although the exact underlying mechanisms remain largely unknown, the heterogeneity between individual patients supports the assumption that D2T RA is a syndrome involving different pathogenic mechanisms.
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Affiliation(s)
- Nadia M T Roodenrijs
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht
| | - Paco M J Welsing
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht
| | - Joël van Roon
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht
| | | | - Marlies C van der Goes
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht
- Department of Rheumatology, Meander Medical Center, Amersfoort, The Netherlands
| | - György Nagy
- Department of Rheumatology & Clinical Immunology
- Department of Genetics, Cell and Immunobiology, Semmelweis University, Budapest, Hungary
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Research & Early Development, South San Francisco, CA, USA
| | - Jacob M van Laar
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht
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4
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Ren Y, Wang L, Dai H, Qiu G, Liu J, Yu D, Liu J, Lyu CZ, Liu L, Zheng M. Genome-wide association analysis of anti-TNF-α treatment response in Chinese patients with psoriasis. Front Pharmacol 2022; 13:968935. [PMID: 36059983 PMCID: PMC9437453 DOI: 10.3389/fphar.2022.968935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background: TNF-α inhibitors are effective biological agents for treating psoriasis, but the treatment responses differ across patients. This study aimed to identify genetic biomarkers of anti-TNF-α response in Chinese psoriasis patients using a genome-wide association approach. Methods: We recruited two independent cohorts of Chinese psoriasis patients administered etanercept biosimilar (with or without methotrexate). We identified 61 and 87 good responders (PASI improvement ≥75%), 19 and 10 poor responders (PASI improvement <50%) after 24 weeks treatment in the two cohorts, respectively. Then we performed genome-wide association studies (GWAS) on anti-TNF-α response in each cohort independently, followed by a fixed-effects inverse-variance meta-analysis in the 148 good and 29 poor responders. Results: We tested genetic associations with >3 million genetic variants in either cohort. Meta-analysis identified significant associations within seven loci at p < 10−5, which also showed consistent association evidence in the two cohorts. These seven loci include rs2431355 (OR = 6.65, p = 4.46 × 10−7, IQGAP2-F2RL2 on 5q13.3), rs11801616 (OR = 0.11, p = 1.75 × 10−6, SDC3 on 1p35.2), rs3754679 (OR = 0.17, p = 7.71 × 10−6, CNOT11 on 2q11.2), rs13166823 (OR = 0.09, p = 3.71 × 10−6, IRF1-AS1 on 5q31.1), rs10220768 (OR = 5.49, p = 1.48 × 10−6, NPAP1 on 15q11.2), rs4796752 (OR = 5.56, p = 1.49 × 10−6, KRT31 on 17q21.2), and rs13045590 (OR = 0.08, p = 9.67 × 10−7, CTSZ on 20q13.3). Of the seven SNPs, six SNPs showed significant eQTL effect (p < 1 × 10−6) for several genes in multiple tissues. Conclusion: These results suggest novel biological mechanisms and potential biomarkers for the response to anti-TNF therapies. These findings warrant further validation.
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Affiliation(s)
- Yunqing Ren
- Department of Dermatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ling Wang
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Huatuo Dai
- Department of Dermatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guiying Qiu
- Department of Dermatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jipeng Liu
- Department of Dermatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
| | - Dianhe Yu
- Department of Dermatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Cheng-Zhi Lyu
- Department of Dermatology, Dalian Dermatosis Hospital, Dalian, China
| | - Lunfei Liu
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Dermatology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
- *Correspondence: Lunfei Liu, ; Min Zheng,
| | - Min Zheng
- Department of Dermatology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Lunfei Liu, ; Min Zheng,
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-Omic Approaches and Treatment Response in Rheumatoid Arthritis. Pharmaceutics 2022; 14:pharmaceutics14081648. [PMID: 36015273 PMCID: PMC9412998 DOI: 10.3390/pharmaceutics14081648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is an inflammatory disorder characterized by an aberrant activation of innate and adaptive immune cells. There are different drugs used for the management of RA, including disease-modifying antirheumatic drugs (DMARDs). However, a significant percentage of RA patients do not initially respond to DMARDs. This interindividual variation in drug response is caused by a combination of environmental, genetic and epigenetic factors. In this sense, recent -omic studies have evidenced different molecular signatures involved in this lack of response. The aim of this review is to provide an updated overview of the potential role of -omic approaches, specifically genomics, epigenomics, transcriptomics, and proteomics, to identify molecular biomarkers to predict the clinical efficacy of therapies currently used in this disorder. Despite the great effort carried out in recent years, to date, there are still no validated biomarkers of response to the drugs currently used in RA. -Omic studies have evidenced significant differences in the molecular profiles associated with treatment response for the different drugs used in RA as well as for different cell types. Therefore, global and cell type-specific -omic studies analyzing response to the complete therapeutical arsenal used in RA, including less studied therapies, such as sarilumab and JAK inhibitors, are greatly needed.
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Gene Ontology Analysis Highlights Biological Processes Influencing Non-Response to Anti-TNF Therapy in Rheumatoid Arthritis. Biomedicines 2022; 10:biomedicines10081808. [PMID: 36009355 PMCID: PMC9404936 DOI: 10.3390/biomedicines10081808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022] Open
Abstract
Anti-TNF therapy has significantly improved disease control in rheumatoid arthritis, but a fraction of rheumatoid arthritis patients do not respond to anti-TNF therapy or lose response over time. Moreover, the mechanisms underlying non-response to anti-TNF therapy remain largely unknown. To date, many single biomarkers of response to anti-TNF therapy have been published but they have not yet been analyzed as a system of interacting nodes. The aim of our study is to systematically elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis using the gene ontologies of previously published predictive biomarkers. Gene networks were constructed based on published biomarkers and then enriched gene ontology terms were elucidated in subgroups using gene ontology software tools. Our results highlight the novel role of proteasome-mediated protein catabolic processes (p = 2.91 × 10−15) and plasma lipoproteins (p = 4.55 × 10−11) in anti-TNF therapy response. The results of our gene ontology analysis help elucidate the biological processes underlying non-response to anti-TNF therapy in rheumatoid arthritis and encourage further study of the highlighted processes.
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White IR, Kleinstein SE, Praet C, Chamberlain C, McHale D, Maia JM, Xie P, Goldstein DB, Urban TJ, Shea PR. A genome-wide screen for variants influencing certolizumab pegol response in a moderate to severe rheumatoid arthritis population. PLoS One 2022; 17:e0261165. [PMID: 35413058 PMCID: PMC9004786 DOI: 10.1371/journal.pone.0261165] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 11/24/2021] [Indexed: 12/14/2022] Open
Abstract
Certolizumab pegol (CZP) is a PEGylated Fc-free tumor necrosis factor (TNF) inhibitor antibody approved for use in the treatment of rheumatoid arthritis (RA), Crohn’s disease, psoriatic arthritis, axial spondyloarthritis and psoriasis. In a clinical trial of patients with severe RA, CZP improved disease symptoms in approximately half of patients. However, variability in CZP efficacy remains a problem for clinicians, thus, the aim of this study was to identify genetic variants predictive of CZP response. We performed a genome-wide association study (GWAS) of 302 RA patients treated with CZP in the REALISTIC trial to identify common single nucleotide polymorphisms (SNPs) associated with treatment response. Whole-exome sequencing was also performed for 74 CZP extreme responders and non-responders within the same population, as well as 1546 population controls. No common SNPs or rare functional variants were significantly associated with CZP response, though a non-significant enrichment in the RA-implicated KCNK5 gene was observed. Two SNPs near spondin-1 and semaphorin-4G approached genome-wide significance. The results of the current study did not provide an unambiguous predictor of CZP response.
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Affiliation(s)
- Ian R. White
- Experimental Medicine and Diagnostics, UCB Celltech, Slough, United Kingdom
| | - Sarah E. Kleinstein
- Institute for Genomic Medicine, Columbia University, New York, New York, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Chris Chamberlain
- Experimental Medicine and Diagnostics, UCB Celltech, Slough, United Kingdom
| | - Duncan McHale
- Experimental Medicine and Diagnostics, UCB Celltech, Slough, United Kingdom
| | - Jessica M. Maia
- Institute for Genomic Medicine, Columbia University, New York, New York, United States of America
| | - Pingxing Xie
- Institute for Genomic Medicine, Columbia University, New York, New York, United States of America
- Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, United States of America
| | - Thomas J. Urban
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Patrick R. Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, United States of America
- * E-mail:
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Xia G, Li Y, Pan W, Qian C, Ma L, Zhou J, Xu H, Cheng C. SLAMF6 is associated with the susceptibility and severity of rheumatoid arthritis in the Chinese population. J Orthop Surg Res 2022; 17:13. [PMID: 35016729 PMCID: PMC8753921 DOI: 10.1186/s13018-021-02901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES A recently published genome-wide association study identified six novel loci associated with rheumatoid arthritis (RA) in Korean population. We aimed to investigate whether these newly reported RA-risk loci are associated with RA in the Chinese population and to further characterize the functional role of the susceptible gene. METHODS The susceptible variants of RA were genotyped in 600 RA patients and 800 healthy controls, including rs148363003 of SLAMF6, rs117605225 of CXCL13, rs360136 of SWAP70, rs111597524 of NFKBIA, rs194757 of ZFP36L1 and rs1547233 of LINC00158. Synovial tissues were collected from the knee joint of 50 RA patients and 40 controls without osteoarthritis for the gene expression analysis. Inter-group comparisons were performed with the Chi-square test for genotyping data or with Student's t-test for gene expression analysis. RESULT For rs148363003 of SLAMF6, RA patients were observed to have a significantly lower frequency of genotype CC (4.5% vs. 0.9%, p = 0.004) as compared with the controls. The frequency of allele C was remarkably higher in the patients than in the controls (11.5% vs. 8.0%, p = 0.002), with an odds ratio of 1.49 (95% CI = 1.16-1.92). There was no significant difference between the patients and the controls regarding genotype or allele frequency of the other 5 variants. The mRNA expression of SLAMF6 was 1.6 folds higher in the RA patients than in the controls. Moreover, SLAMF6 expression was 1.5 folds higher in patients with genotype CC than in the patients with genotype TT. CONCLUSIONS SLAMF6 was associated with both the susceptibility and severity of RA in the Chinese population. Moreover, rs148363003 could be a functional variant regulating the tissue expression of SLAMF6 in RA patients. It is advisable to conduct further functional analysis for a comprehensive knowledge on the contribution of this variant to the development of RA.
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Affiliation(s)
- Guodong Xia
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China
| | - Yetian Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei City, China
| | - Wei Pan
- Department of Orthopaedic Surgery, The Huai'an Second People's Hospital, Huai'an City, China
| | - Chengmei Qian
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China
| | - Lin Ma
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China
| | - Jingli Zhou
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China
| | - Henggui Xu
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China
| | - Chen Cheng
- Department of Orthopaedic Surgery, The JiangYan TCM Hospital of Taizhou City, JiangYan Road No. 699, Taizhou City, 225500, China.
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Sánchez-Maldonado JM, Cáliz R, López-Nevot MÁ, Cabrera-Serrano AJ, Moñiz-Díez A, Canhão H, Ter Horst R, Quartuccio L, Sorensen SB, Glintborg B, Hetland ML, Filipescu I, Pérez-Pampin E, Conesa-Zamora P, Swierkot J, den Broeder AA, De Vita S, Petersen ERB, Li Y, Ferrer MA, Escudero A, Netea MG, Coenen MJH, Andersen V, Fonseca JE, Jurado M, Bogunia-Kubik K, Collantes E, Sainz J. Validation of GWAS-Identified Variants for Anti-TNF Drug Response in Rheumatoid Arthritis: A Meta-Analysis of Two Large Cohorts. Front Immunol 2021; 12:672255. [PMID: 34777329 PMCID: PMC8579100 DOI: 10.3389/fimmu.2021.672255] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/11/2021] [Indexed: 12/29/2022] Open
Abstract
We aimed to validate the association of 28 GWAS-identified genetic variants for response to TNF inhibitors (TNFi) in a discovery cohort of 1361 rheumatoid arthritis (RA) patients monitored in routine care and ascertained through the REPAIR consortium and DANBIO registry. We genotyped selected markers and evaluated their association with response to TNFi after 6 months of treatment according to the change in disease activity score 28 (ΔDAS28). Next, we confirmed the most interesting results through meta-analysis of our data with those from the DREAM cohort that included 706 RA patients treated with TNFi. The meta-analysis of the discovery cohort and DREAM registry including 2067 RA patients revealed an overall association of the LINC02549rs7767069 SNP with a lower improvement in DAS28 that remained significant after correction for multiple testing (per-allele ORMeta=0.83, PMeta=0.000077; PHet=0.61). In addition, we found that each copy of the LRRC55rs717117G allele was significantly associated with lower improvement in DAS28 in rheumatoid factor (RF)-positive patients (per-allele ORMeta=0.67, P=0.00058; PHet=0.06) whereas an opposite but not significant effect was detected in RF-negative subjects (per-allele ORMeta=1.38, P=0.10; PHet=0.45; PInteraction=0.00028). Interestingly, although the identified associations did not survive multiple testing correction, the meta-analysis also showed overall and RF-specific associations for the MAFBrs6071980 and CNTN5rs1813443 SNPs with decreased changes in DAS28 (per-allele ORMeta_rs6071980 = 0.85, P=0.0059; PHet=0.63 and ORMeta_rs1813443_RF+=0.81, P=0.0059; PHet=0.69 and ORMeta_rs1813443_RF-=1.00, P=0.99; PHet=0.12; PInteraction=0.032). Mechanistically, we found that subjects carrying the LINC02549rs7767069T allele had significantly increased numbers of CD45RO+CD45RA+ T cells (P=0.000025) whereas carriers of the LINC02549rs7767069T/T genotype showed significantly increased levels of soluble scavengers CD5 and CD6 in serum (P=0.00037 and P=0.00041). In addition, carriers of the LRRC55rs717117G allele showed decreased production of IL6 after stimulation of PBMCs with B burgdorferi and E coli bacteria (P=0.00046 and P=0.00044), which suggested a reduced IL6-mediated anti-inflammatory effect of this marker to worsen the response to TNFi. In conclusion, this study confirmed the influence of the LINC02549 and LRRC55 loci to determine the response to TNFi in RA patients and suggested a weak effect of the MAFB and CNTN5 loci that need to be further investigated.
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Affiliation(s)
- Jose Manuel Sánchez-Maldonado
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Rafael Cáliz
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Department of Rheumatology, Virgen de las Nieves University Hospital, Granada, Spain
| | - Miguel Ángel López-Nevot
- Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Immunology Department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Antonio José Cabrera-Serrano
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Ana Moñiz-Díez
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Helena Canhão
- EpiDoC Unit, CEDOC, NOVA Medical School and National School of Public Health, Universidade Nova de Lisboa, Lisbon, Portugal.,Comprehensive Health Research Center (CHRC), NOVA Medical School, Lisbon, Portugal
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
| | - Luca Quartuccio
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy
| | - Signe B Sorensen
- Molecular Diagnostic and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Molecular Medicine, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Bente Glintborg
- The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (DANBIO) Registry, The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Merete L Hetland
- The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (DANBIO) Registry, The Danish Rheumatologic Biobank and Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet, Glostrup, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ileana Filipescu
- Rheumatology Department, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj-Napoca, Romania
| | - Eva Pérez-Pampin
- Rheumatology Unit, University Hospital of Santiago de Compostela, Santiago de Compostela, Spain
| | - Pablo Conesa-Zamora
- Clinical Analysis Department, Santa Lucía University Hospital, Cartagena, Spain
| | - Jerzy Swierkot
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Alfons A den Broeder
- Radboud Institute for Health Sciences, Department of Rheumatology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Salvatore De Vita
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy
| | - Eva Rabing Brix Petersen
- Department of Biochemistry and Immunology, University Hospital of Southern Jutland, Aabenraa, Denmark
| | - Yang Li
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands.,Centre for Individualised Infection Medicine (CiiM) & Centre for Experimental and Clinical Infection Research (TWINCORE), Helmholtz-Centre for Infection Research (HZI) and The Hannover Medical School (MHH), Hannover, Germany
| | - Miguel A Ferrer
- Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Alejandro Escudero
- Rheumatology Department, Reina Sofía Hospital/Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)/University of Córdoba, Córdoba, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands.,Department for Immunology & Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Marieke J H Coenen
- Radboud Institute for Health Sciences, Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vibeke Andersen
- Department of Medical Area, Clinic of Rheumatology, University of Udine, Udine, Italy.,Molecular Diagnostic and Clinical Research Unit, IRS-Center Sonderjylland, University Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Regional Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - João E Fonseca
- Rheumatology and Metabolic Bone Diseases Department, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHLN), Lisbon, Portugal.,Rheumatology Research Unit, Instituto de Medicina Molecular, Faculty of Medicine, University of Lisbon, Lisbon Academic Medical Center, Lisbon, Portugal
| | - Manuel Jurado
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain
| | - Katarzyna Bogunia-Kubik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Eduardo Collantes
- Rheumatology Department, Reina Sofía Hospital/Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)/University of Córdoba, Córdoba, Spain
| | - Juan Sainz
- Genomic Oncology Area, Centre for Genomics and Oncological Research (GENYO), Parque tecnológico de la Salud (PTS) Granada, Granada, Spain.,Hematology Department, Virgen de las Nieves University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria (IBs) Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
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10
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Hashimoto T, Yoshida K, Hashiramoto A, Matsui K. Cell-Free DNA in Rheumatoid Arthritis. Int J Mol Sci 2021; 22:8941. [PMID: 34445645 PMCID: PMC8396202 DOI: 10.3390/ijms22168941] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
Endogenous DNA derived from the nuclei or mitochondria is released into the bloodstream following cell damage or death. Extracellular DNA, called cell-free DNA (cfDNA), is associated with various pathological conditions. Recently, multiple aspects of cfDNA have been assessed, including cfDNA levels, integrity, methylation, and mutations. Rheumatoid arthritis (RA) is the most common form of autoimmune arthritis, and treatment of RA has highly varied outcomes. cfDNA in patients with RA is elevated in peripheral blood and synovial fluid and is associated with disease activity. Profiling of cfDNA in patients with RA may then be utilized in various aspects of clinical practice, such as the prediction of prognosis and treatment responses; monitoring disease state; and as a diagnostic marker. In this review, we discuss cfDNA in patients with RA, particularly the sources of cfDNA and the correlation of cfDNA with RA pathogenesis. We also highlight the potential of analyzing cfDNA profiles to guide individualized treatment approaches for RA.
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Affiliation(s)
- Teppei Hashimoto
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
| | - Kohsuke Yoshida
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Akira Hashiramoto
- Department of Biophysics, Kobe University Graduate School of Health Sciences, Kobe 6540142, Japan; (K.Y.); (A.H.)
| | - Kiyoshi Matsui
- Division of Diabetes, Endocrinology and Clinical Immunology, Department of Internal Medicine, Hyogo College of Medicine, Nishinomiya 6638501, Japan;
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11
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Puentes-Osorio Y, Amariles P, Calleja MÁ, Merino V, Díaz-Coronado JC, Taborda D. Potential clinical biomarkers in rheumatoid arthritis with an omic approach. AUTOIMMUNITY HIGHLIGHTS 2021; 12:9. [PMID: 34059137 PMCID: PMC8165788 DOI: 10.1186/s13317-021-00152-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022]
Abstract
Objective To aid in the selection of the most suitable therapeutic option in patients with diagnosis of rheumatoid arthritis according to the phase of disease, through the review of articles that identify omics biological markers. Methods A systematic review in PubMed/Medline databases was performed. We searched articles from August 2014 to September 2019, in English and Spanish, filtered by title and full text; and using the terms "Biomarkers" AND “Rheumatoid arthritis". Results This article supplies an exhaustive review from research of objective measurement, omics biomarkers and how disease activity appraise decrease unpredictability in treatment determinations, and finally, economic, and clinical outcomes of treatment options by biomarkers’ potential influence. A total of 122 articles were included. Only 92 met the established criteria for review purposes and 17 relevant references about the topic were included as well. Therefore, it was possible to identify 196 potential clinical biomarkers: 22 non-omics, 20 epigenomics, 33 genomics, 21 transcriptomics, 78 proteomics, 4 glycomics, 1 lipidomics and 17 metabolomics. Conclusion A biomarker is a measurable indicator of some, biochemical, physiological, or morphological condition; evaluable at a molecular, biochemical, or cellular level. Biomarkers work as indicators of physiological or pathological processes, or as a result of a therapeutic management. In the last five years, new biomarkers have been identified, especially the omics, which are those that proceed from the investigation of genes (genomics), metabolites (metabolomics), and proteins (proteomics). These biomarkers contribute to the physician choosing the best therapeutic option in patients with rheumatoid arthritis.
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12
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Mezghiche I, Yahia-Cherbal H, Rogge L, Bianchi E. Novel approaches to develop biomarkers predicting treatment responses to TNF-blockers. Expert Rev Clin Immunol 2021; 17:331-354. [PMID: 33622154 DOI: 10.1080/1744666x.2021.1894926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: Chronic inflammatory diseases (CIDs) cause significant morbidity and are a considerable burden for the patients in terms of pain, impaired function, and diminished quality of life. Important progress in CID treatment has been obtained with biological therapies, such as tumor-necrosis-factor blockers. However, more than a third of the patients fail to respond to these inhibitors and are exposed to the side effects of treatment, without the benefits. Therefore, there is a strong interest in developing tools to predict response of patients to biologics. Areas covered: The authors searched PubMed for recent studies on biomarkers for disease assessment and prediction of therapeutic responses, focusing on the effect of TNF blockers on immune responses in spondyloarthritis (SpA), and other CID, in particular rheumatoid arthritis and inflammatory bowel disease. Conclusions will be drawn about the possible development of predictive biomarkers for response to treatment. Expert opinion: No validated biomarker is currently available to predict treatment response in CID. New insight could be generated through the development of new bioinformatic modeling approaches to combine multidimensional biomarkers that explain the different genetic, immunological and environmental determinants of therapeutic responses.
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Affiliation(s)
- Ikram Mezghiche
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Université De Paris, Sorbonne Paris Cité, Paris, France
| | - Hanane Yahia-Cherbal
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Fondation AP-HP, Paris, France
| | - Lars Rogge
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Elisabetta Bianchi
- Department of Immunology, Immunoregulation Unit, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
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13
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Abstract
Patients with inflammatory bowel disease (IBD) show large variability in disease course, and also treatment response. The variability in treatment response has led to many initiatives in search of genetic markers to optimize treatment and avoid severe side effects. This has been very successful for thiopurines, one of the drugs used to induce and maintain remission in IBD. However, for the newer treatment options for IBD, like biologicals, the search for genetic predictors has not yielded any candidate biomarkers with clinical utility. In this review, a summary of recent advances in pharmacogenetics focusing on thiopurines and anti-TNF agents is given.
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Affiliation(s)
- Bianca Jc van den Bosch
- Deparment of Clinical Genetics, Maastricht University Medical Center, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Marieke Jh Coenen
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, P.O. Box 9101, 6500HB, Nijmegen, The Netherlands
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14
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Hassan R, Allali I, Agamah FE, Elsheikh SSM, Thomford NE, Dandara C, Chimusa ER. Drug response in association with pharmacogenomics and pharmacomicrobiomics: towards a better personalized medicine. Brief Bioinform 2020; 22:6012864. [PMID: 33253350 DOI: 10.1093/bib/bbaa292] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/19/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Researchers have long been presented with the challenge imposed by the role of genetic heterogeneity in drug response. For many years, Pharmacogenomics and pharmacomicrobiomics has been investigating the influence of an individual's genetic background to drug response and disposition. More recently, the human gut microbiome has proven to play a crucial role in the way patients respond to different therapeutic drugs and it has been shown that by understanding the composition of the human microbiome, we can improve the drug efficacy and effectively identify drug targets. However, our knowledge on the effect of host genetics on specific gut microbes related to variation in drug metabolizing enzymes, the drug remains limited and therefore limits the application of joint host-microbiome genome-wide association studies. In this paper, we provide a historical overview of the complex interactions between the host, human microbiome and drugs. While discussing applications, challenges and opportunities of these studies, we draw attention to the critical need for inclusion of diverse populations and the development of an innovative and combined pharmacogenomics and pharmacomicrobiomics approach, that may provide an important basis in personalized medicine.
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Affiliation(s)
- Radia Hassan
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Imane Allali
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | | | - Nicholas E Thomford
- Lecturers at the Department of Medical Biochemistry School of Medical Sciences, University of Cape Coast, Ghana
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town
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15
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Mikhaylenko DS, Nemtsova MV, Bure IV, Kuznetsova EB, Alekseeva EA, Tarasov VV, Lukashev AN, Beloukhova MI, Deviatkin AA, Zamyatnin AA. Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response. Int J Mol Sci 2020; 21:E4911. [PMID: 32664585 PMCID: PMC7402327 DOI: 10.3390/ijms21144911] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthropathy worldwide. Possible manifestations of RA can be represented by a wide variability of symptoms, clinical forms, and course options. This multifactorial disease is triggered by a genetic predisposition and environmental factors. Both clinical and genealogical studies have demonstrated disease case accumulation in families. Revealing the impact of candidate gene missense variants on the disease course elucidates understanding of RA molecular pathogenesis. A multivariate genomewide association study (GWAS) based analysis identified the genes and signalling pathways involved in the pathogenesis of the disease. However, these identified RA candidate gene variants only explain 30% of familial disease cases. The genetic causes for a significant proportion of familial RA have not been determined until now. Therefore, it is important to identify RA risk groups in different populations, as well as the possible prognostic value of some genetic variants for disease development, progression, and treatment. Our review has two purposes. First, to summarise the data on RA candidate genes and the increased disease risk associated with these alleles in various populations. Second, to describe how the genetic variants can be used in the selection of drugs for the treatment of RA.
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Affiliation(s)
- Dmitry S. Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Irina V. Bure
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Ekaterina A. Alekseeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Vadim V. Tarasov
- Department of Pharmacology and Pharmacy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alexander N. Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Marina I. Beloukhova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrei A. Deviatkin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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16
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Khoury T, Ilan Y. Introducing Patterns of Variability for Overcoming Compensatory Adaptation of the Immune System to Immunomodulatory Agents: A Novel Method for Improving Clinical Response to Anti-TNF Therapies. Front Immunol 2019; 10:2726. [PMID: 31824506 PMCID: PMC6879658 DOI: 10.3389/fimmu.2019.02726] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Primary lack of response and secondary loss of response (LOR) are major obstacles to the use of anti–tumor necrosis factor (TNF)-based therapies in patients with rheumatoid arthritis or inflammatory bowel disease. Here, we review the mechanisms and methods for predicting LOR and the currently used methods for overcoming the ineffectiveness of anti-TNFs. The complex functions of TNF and anti-TNF antibodies, which can promote both pro- or anti-inflammatory actions, and the factors that affect the induction of immune tolerance to their effects are presented. The lack of rules and the continuous dynamics of the immune processes partly underlie the unpredictability of the response to anti-TNFs. Variability is inherent to biological systems, including immune processes, and intra/inter-patient variability has been described in the response to drugs. This variability is viewed as a compensatory adaptation mechanism of the immune system in response to drugs and may contribute to treatment LOR. Dose reductions and drug holidays have been tested in patients treated with anti-TNFs. Regular dose-based regimens may be incompatible with physiological variability, further contributing to treatment inefficacy. We present the concept of overcoming immune system adaptation to anti-TNFs by introducing patient-tailored patterns of variability to treatment regimens.
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Affiliation(s)
- Tawfik Khoury
- Department of Gastroenterology, Galilee Medical Center, Nahariya, Israel.,Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Yaron Ilan
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
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17
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Aterido A, Cañete JD, Tornero J, Blanco F, Fernández-Gutierrez B, Pérez C, Alperi-López M, Olivè A, Corominas H, Martínez-Taboada V, González I, Fernández-Nebro A, Erra A, López-Lasanta M, López Corbeto M, Palau N, Marsal S, Julià A. A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. Front Immunol 2019; 10:1459. [PMID: 31312201 PMCID: PMC6614444 DOI: 10.3389/fimmu.2019.01459] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Rheumatoid arthritis (RA) is the most frequent autoimmune disease involving the joints. Although anti-TNF therapies have proven effective in the management of RA, approximately one third of patients do not show a significant clinical response. The objective of this study was to identify new genetic variation associated with the clinical response to anti-TNF therapy in RA. Methods: We performed a sequential multi-omic analysis integrating different sources of molecular information. First, we extracted the RNA from synovial biopsies of 11 RA patients starting anti-TNF therapy to identify gene coexpression modules (GCMs) in the RA synovium. Second, we analyzed the transcriptomic association between each GCM and the clinical response to anti-TNF therapy. The clinical response was determined at week 14 using the EULAR criteria. Third, we analyzed the association between the GCMs and anti-TNF response at the genetic level. For this objective, we used genome-wide data from a cohort of 348 anti-TNF treated patients from Spain. The GCMs that were significantly associated with the anti-TNF response were then tested for validation in an independent cohort of 2,706 anti-TNF treated patients. Finally, the functional implication of the validated GCMs was evaluated via pathway and cell type epigenetic enrichment analyses. Results: A total of 149 GCMs were identified in the RA synovium. From these, 13 GCMs were found to be significantly associated with anti-TNF response (P < 0.05). At the genetic level, we detected two of the 13 GCMs to be significantly associated with the response to adalimumab (P = 0.0015) and infliximab (P = 0.021) in the Spain cohort. Using the independent cohort of RA patients, we replicated the association of the GCM associated with the response to adalimumab (P = 0.0019). The validated module was found to be significantly enriched for genes involved in the nucleotide metabolism (P = 2.41e-5) and epigenetic marks from immune cells, including CD4+ regulatory T cells (P = 0.041). Conclusions: These findings show the existence of a drug-specific genetic basis for anti-TNF response, thereby supporting treatment stratification in the search for response biomarkers in RA.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Juan D Cañete
- Rheumatology Department, Hospital Clínic de Barcelona and Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Jesús Tornero
- Rheumatology Department, Hospital Universitario De Guadalajara, Guadalajara, Spain
| | - Francisco Blanco
- Rheumatology Department, INIBIC-Hospital Universitario A Coruña, A Coruña, Spain
| | | | - Carolina Pérez
- Rheumatology Department, Parc de Salut Mar, Barcelona, Spain
| | | | - Alex Olivè
- Rheumatology Department, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Héctor Corominas
- Rheumatology Department, Hospital Moisès Broggi, Barcelona, Spain
| | | | - Isidoro González
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | - Antonio Fernández-Nebro
- UGC Reumatología, Instituto Investigación Biomédica Málaga, Hospital Regional Universitario, Universidad de Málaga, Málaga, Spain
| | - Alba Erra
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
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18
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Evaluation of 12 GWAS-drawn SNPs as biomarkers of rheumatoid arthritis response to TNF inhibitors. A potential SNP association with response to etanercept. PLoS One 2019; 14:e0213073. [PMID: 30818333 PMCID: PMC6395028 DOI: 10.1371/journal.pone.0213073] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/14/2019] [Indexed: 12/14/2022] Open
Abstract
Research in rheumatoid arthritis (RA) is increasingly focused on the discovery of biomarkers that could enable personalized treatments. The genetic biomarkers associated with the response to TNF inhibitors (TNFi) are among the most studied. They include 12 SNPs exhibiting promising results in the three largest genome-wide association studies (GWAS). However, they still require further validation. With this aim, we assessed their association with response to TNFi in a replication study, and a meta-analysis summarizing all non-redundant data. The replication involved 755 patients with RA that were treated for the first time with a biologic drug, which was either infliximab (n = 397), etanercept (n = 155) or adalimumab (n = 203). Their DNA samples were successfully genotyped with a single-base extension multiplex method. Lamentably, none of the 12 SNPs was associated with response to the TNFi in the replication study (p > 0.05). However, a drug-stratified exploratory analysis revealed a significant association of the NUBPL rs2378945 SNP with a poor response to etanercept (B = -0.50, 95% CI = -0.82, -0.17, p = 0.003). In addition, the meta-analysis reinforced the previous association of three SNPs: rs2378945, rs12142623, and rs4651370. In contrast, five of the remaining SNPs were less associated than before, and the other four SNPs were no longer associated with the response to treatment. In summary, our results highlight the complexity of the pharmacogenetics of TNFi in RA showing that it could involve a drug-specific component and clarifying the status of the 12 GWAS-drawn SNPs.
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19
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Okada Y, Eyre S, Suzuki A, Kochi Y, Yamamoto K. Genetics of rheumatoid arthritis: 2018 status. Ann Rheum Dis 2018; 78:446-453. [PMID: 30530827 DOI: 10.1136/annrheumdis-2018-213678] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Study of the genetics of rheumatoid arthritis (RA) began about four decades ago with the discovery of HLA-DRB1 Since the beginning of this century, a number of non-HLA risk loci have been identified through genome-wide association studies (GWAS). We now know that over 100 loci are associated with RA risk. Because genetic information implies a clear causal relationship to the disease, research into the pathogenesis of RA should be promoted. However, only 20% of GWAS loci contain coding variants, with the remaining variants occurring in non-coding regions, and therefore, the majority of causal genes and causal variants remain to be identified. The use of epigenetic studies, high-resolution mapping of open chromatin, chromosomal conformation technologies and other approaches could identify many of the missing links between genetic risk variants and causal genetic components, thus expanding our understanding of RA genetics.
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Affiliation(s)
- Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Stephen Eyre
- Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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20
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Lopez-Rodriguez R, Perez-Pampin E, Marquez A, Blanco FJ, Joven B, Carreira P, Ferrer MA, Caliz R, Valor L, Narvaez J, Cañete JD, Ordoñez MDC, Manrique-Arija S, Vasilopoulos Y, Balsa A, Pascual-Salcedo D, Moreno-Ramos MJ, Alegre-Sancho JJ, Navarro-Sarabia F, Moreira V, Garcia-Portales R, Raya E, Magro-Checa C, Martin J, Gomez-Reino JJ, Gonzalez A. Validation study of genetic biomarkers of response to TNF inhibitors in rheumatoid arthritis. PLoS One 2018; 13:e0196793. [PMID: 29734345 PMCID: PMC5937760 DOI: 10.1371/journal.pone.0196793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 11/19/2022] Open
Abstract
Genetic biomarkers are sought to personalize treatment of patients with rheumatoid arthritis (RA), given their variable response to TNF inhibitors (TNFi). However, no genetic biomaker is yet sufficiently validated. Here, we report a validation study of 18 previously reported genetic biomarkers, including 11 from GWAS of response to TNFi. The validation was attempted in 581 patients with RA that had not been treated with biologic antirheumatic drugs previously. Their response to TNFi was evaluated at 3, 6 and 12 months in two ways: change in the DAS28 measure of disease activity, and according to the EULAR criteria for response to antirheumatic drugs. Association of these parameters with the genotypes, obtained by PCR amplification followed by single-base extension, was tested with regression analysis. These analyses were adjusted for baseline DAS28, sex, and the specific TNFi. However, none of the proposed biomarkers was validated, as none showed association with response to TNFi in our study, even at the time of assessment and with the outcome that showed the most significant result in previous studies. These negative results are notable because this was the first independent validation study for 12 of the biomarkers, and because they indicate that prudence is needed in the interpretation of the proposed biomarkers of response to TNFi even when they are supported by very low p values. The results also emphasize the requirement of independent replication for validation, and the need to search protocols that could increase reproducibility of the biomarkers of response to TNFi.
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Affiliation(s)
- Rosario Lopez-Rodriguez
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Eva Perez-Pampin
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Ana Marquez
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - Francisco J. Blanco
- Rheumatology Department, Instituto de Investigacion Biomedica–Complejo Hospitalario Universitario A Coruna, Coruna, Spain
| | | | | | - Miguel Angel Ferrer
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Rafael Caliz
- Rheumatology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Lara Valor
- Rheumatology Unit, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Javier Narvaez
- Department of Rheumatology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Juan D. Cañete
- Arthritis Unit, Rheumatology Dpt, Hospital Clinic and IDIBAPS, Barcelona, Spain
| | - Maria del Carmen Ordoñez
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga Spain
| | - Sara Manrique-Arija
- Servicio de Reumatología, HRU Carlos Haya, Universidad de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga Spain
| | - Yiannis Vasilopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Alejandro Balsa
- Rheumatology Unit, Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), Hospital Universitario La Paz, Madrid, Spain
| | - Dora Pascual-Salcedo
- Department of Immunology, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | | | | | - Virginia Moreira
- Rheumatology Unit, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | | | - Enrique Raya
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
| | - Cesar Magro-Checa
- Department of Rheumatology, Hospital Clínico San Cecilio, Granada, Spain
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Granada, Spain
| | - Juan J. Gomez-Reino
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Experimental and Observational Rheumatology and Rheumatology Unit, Instituto de Investigación Sanitaria, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain
- * E-mail:
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Arshad M, Bhatti A, John P, Jalil F, Williams RO. Association of rs182429 variant in TAGAP with rheumatoid arthritis in Pakistani population. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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22
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Cui J, Diogo D, Stahl EA, Canhao H, Mariette X, Greenberg JD, Okada Y, Pappas DA, Fulton RS, Tak PP, Nurmohamed MT, Lee A, Larson DE, Kurreeman F, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Mardis ER, van der Horst-Bruinsma IE, Wolbink GJ, Gregersen PK, Kremer JM, Crusius JBA, de Vries N, Huizinga TWJ, Fonseca JE, Miceli-Richard C, Karlson EW, Coenen MJH, Barton A, Plenge RM, Raychaudhuri S. Brief Report: The Role of Rare Protein-Coding Variants in Anti-Tumor Necrosis Factor Treatment Response in Rheumatoid Arthritis. Arthritis Rheumatol 2017; 69:735-741. [PMID: 27788309 DOI: 10.1002/art.39966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
OBJECTIVE In many rheumatoid arthritis (RA) patients, disease is controlled with anti-tumor necrosis factor (anti-TNF) biologic therapies. However, in a significant number of patients, the disease fails to respond to anti-TNF therapy. We undertook the present study to examine the hypothesis that rare and low-frequency genetic variants might influence response to anti-TNF treatment. METHODS We sequenced the coding region of 750 genes in 1,094 RA patients of European ancestry who were treated with anti-TNF. After quality control, 690 genes were included in the analysis. We applied single-variant association and gene-based association tests to identify variants associated with anti-TNF treatment response. In addition, given the key mechanistic role of TNF, we performed gene set analyses of 27 TNF pathway genes. RESULTS We identified 14,420 functional variants, of which 6,934 were predicted as nonsynonymous 2,136 of which were further predicted to be "damaging." Despite the fact that the study was well powered, no single variant or gene showed study-wide significant association with change in the outcome measures disease activity or European League Against Rheumatism response. Intriguingly, we observed 3 genes, of 27 with nominal signals of association (P < 0.05), that were involved in the TNF signaling pathway. However, when we performed a rigorous gene set enrichment analysis based on association P value ranking, we observed no evidence of enrichment of association at genes involved in the TNF pathway (Penrichment = 0.15, based on phenotype permutations). CONCLUSION Our findings suggest that rare and low-frequency protein-coding variants in TNF signaling pathway genes or other genes do not contribute substantially to anti-TNF treatment response in patients with RA.
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Affiliation(s)
- Jing Cui
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dorothee Diogo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Eli A Stahl
- Mount Sinai School of Medicine, New York, New York
| | | | - Xavier Mariette
- Université Paris Sud, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, Bicêtre Hospital, AP-HP, Paris, France
| | | | - Yukinori Okada
- Osaka University Graduate School of Medicine, Osaka, Japan
| | | | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Paul P Tak
- University of Amsterdam, Amsterdam, The Netherlands
| | | | - Annette Lee
- Feinstein Institute for Medical Research, Manhasset, New York
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Fina Kurreeman
- Leiden University Medical Centre, Leiden, The Netherlands
| | - Tracie L Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Lucinda L Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | - Gert-Jan Wolbink
- Amsterdam Rheumatology and Immunology Center, Reade, Amsterdam, The Netherlands
| | | | - Joel M Kremer
- Albany Medical College and the Center for Rheumatology, Albany, New York
| | | | | | | | | | | | | | | | - Anne Barton
- Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Robert M Plenge
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, Broad Institute, Cambridge, Massachusetts, and Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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23
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Bek S, Bojesen AB, Nielsen JV, Sode J, Bank S, Vogel U, Andersen V. Systematic review and meta-analysis: pharmacogenetics of anti-TNF treatment response in rheumatoid arthritis. THE PHARMACOGENOMICS JOURNAL 2017; 17:403-411. [PMID: 28607508 PMCID: PMC5637244 DOI: 10.1038/tpj.2017.26] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/08/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease that affects ~1% of the Caucasian population. Over the last decades, the availability of biological drugs targeting the proinflammatory cytokine tumour necrosis factor α, anti-TNF drugs, has improved the treatment of patients with RA. However, one-third of the patients do not respond to the treatment. We wanted to evaluate the status of pharmacogenomics of anti-TNF treatment. We performed a PubMed literature search and all studies reporting original data on associations between genetic variants and anti-TNF treatment response in RA patients were included and results evaluated by meta-analysis. In total, 25 single nucleotide polymorphisms were found to be associated with anti-TNF treatment response in RA (19 from genome-wide association studies and 6 from the meta-analyses), and these map to genes involved in T cell function, NFκB and TNF signalling pathways (including CTCN5, TEC, PTPRC, FCGR2A, NFKBIB, FCGR2A, IRAK3). Explorative prediction analyses found that biomarkers for clinical treatment selection are not yet available.
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Affiliation(s)
- S Bek
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - A B Bojesen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark.,Research Unit for E-mental Health, Mental Health Services in the Region of Southern Odense, Odense, Denmark
| | - J V Nielsen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - J Sode
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - S Bank
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark
| | - U Vogel
- Research Unit for E-mental Health, Mental Health Services in the Region of Southern Odense, Odense, Denmark.,National Research Centre for the Working Environment, Copenhagen, Denmark
| | - V Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.,Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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Funahashi K, Koyano S, Echizen H, Matsubara T. Whole genome analysis on the genetic backgrounds associated with the secondary failure to etanercept in patients with rheumatoid arthritis. Mod Rheumatol 2016; 27:271-277. [PMID: 27416107 DOI: 10.1080/14397595.2016.1206172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES Etanercept is effective for the treatment of rheumatoid arthritis (RA). However, some of the patients eventually lose efficacy (secondary failure) despite the absence of neutralizing antibodies. We aimed to explore single nucleotide polymorphisms (SNPs) associated with secondary failure. METHODS We recruited RA patients given etanercept at 50 mg/week for ≥6 months from the Matsubara Mayflower Hospital RA registry. They were assigned to responders, secondary failure patients, and non-responders according to Disease Activity Score. Genome-wide association study (GWAS) was performed using Illumina HumanHAP300k BeadChips and the results were analyzed with Plink software. Clinical backgrounds were compared by ANOVA and contingency table analysis. The protocol was approved by IRB and written informed consent was obtained. RESULTS Ninety, 27 and 17 patients were assigned to responders, secondary failure patients, and non-responders, respectively. No significant differences were observed regarding clinical backgrounds among the groups. GWAS revealed that six and 37 SNPs may be associated with secondary failure to etanercept with p< 10-6 and <10-5, respectively. CONCLUSION While our preliminary results with borderline significance should be validated by studies with a greater population size, some of the SNPs detected by our GWAS may be involved in the development of secondary failure to etanercept.
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Affiliation(s)
- Keiko Funahashi
- a Department of Clinical Research , Matsubara Mayflower Hospital Kato , Hyogo , Japan
| | - Satoru Koyano
- b Research Institute of Joint Disease Kobe , Hyogo , Japan and
| | - Hirotoshi Echizen
- c Department of Pharmacotherapy , Meiji Pharmaceutical University Kiyose , Tokyo , Japan
| | - Tsukasa Matsubara
- a Department of Clinical Research , Matsubara Mayflower Hospital Kato , Hyogo , Japan.,b Research Institute of Joint Disease Kobe , Hyogo , Japan and
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Smith SL, Plant D, Lee XH, Massey J, Hyrich K, Morgan AW, Wilson AG, Isaacs J, Barton A. Previously reported PDE3A-SLCO1C1 genetic variant does not correlate with anti-TNF response in a large UK rheumatoid arthritis cohort. Pharmacogenomics 2016; 17:715-20. [PMID: 27180831 PMCID: PMC4996314 DOI: 10.2217/pgs.16.16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIM A genetic variant has recently reached genome-wide significance for association with TNF-inhibitor response in rheumatoid arthritis patients. Here we undertake a replication study in a UK Caucasian population to test for association with TNF-inhibitor response. MATERIALS & METHODS The genetic variant, rs3794271, located within the PDE3A-SLCO1C1 locus was analyzed for correlation with treatment response using both the EULAR classification criteria and absolute change in (Δ)DAS28 scores as outcome measures. RESULTS Genotype data were available from 1750 TNF-inhibitor treated individuals. However, no evidence for association was observed (EULAR: p = 0.91 and ΔDAS28: p = 0.93). Furthermore, no significant associations were observed upon stratification by the anti-TNF received (p > 0.05). CONCLUSION In the largest replication cohort conducted to date, no evidence for association was observed.
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Affiliation(s)
- Samantha Louise Smith
- Arthritis Research UK, Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Darren Plant
- NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust & University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Xiu Hue Lee
- Arthritis Research UK, Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Jonathan Massey
- Arthritis Research UK, Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Kimme Hyrich
- Arthritis Research UK, Centre for Epidemiology, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK
| | - Ann W Morgan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, UK
| | - Anthony G Wilson
- UCD School of Medicine & Medical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - John Isaacs
- NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne NHS Foundation Trust & Newcastle University, Newcastle-upon-Tyne, UK
| | - Anne Barton
- Arthritis Research UK, Centre for Genetics & Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Sciences Centre, The University of Manchester, Manchester, UK.,NIHR Manchester Musculoskeletal BRU, Central Manchester Foundation Trust & University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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Márquez A, Martín J, Carmona FD. Emerging aspects of molecular biomarkers for diagnosis, prognosis and treatment response in rheumatoid arthritis. Expert Rev Mol Diagn 2016; 16:663-75. [DOI: 10.1080/14737159.2016.1174579] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Honne K, Hallgrímsdóttir I, Wu C, Sebro R, Jewell NP, Sakurai T, Iwamoto M, Minota S, Jawaheer D. A longitudinal genome-wide association study of anti-tumor necrosis factor response among Japanese patients with rheumatoid arthritis. Arthritis Res Ther 2016; 18:12. [PMID: 26776603 PMCID: PMC4718049 DOI: 10.1186/s13075-016-0920-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/04/2016] [Indexed: 12/17/2022] Open
Abstract
Background Studies of Caucasian patients with rheumatoid arthritis (RA) to identify genetic biomarkers of anti-tumor necrosis factor (TNF) response have used response at a single time point as the phenotype with which single nucleotide polymorphism (SNP) associations have been tested. The findings have been inconsistent across studies. Among Japanese patients, only a few SNPs have been investigated. We report here the first genome-wide association study (GWAS) to identify genetic biomarkers of anti-TNF response among Japanese RA patients, using response at 2 time-points for a more reliable clinical phenotype over time. Methods Disease Activity Scores based on 28 joint counts (DAS28) were assessed at baseline (before initial therapy), and after 3 and 6 months in 487 Japanese RA patients starting anti-TNF therapy for the first time or switching to a new anti-TNF agent. A genome-wide panel of SNPs was genotyped and additional SNPs were imputed. Using change in DAS28 scores from baseline at both 3 (ΔDAS-3) and 6 months (ΔDAS-6) as the response phenotype, a longitudinal genome-wide association analysis was conducted using generalized estimating equations (GEE) models, adjusting for baseline DAS28, treatment duration, type of anti-TNF agent and concomitant methotrexate. Cross-sectional analyses were performed using multivariate linear regression models, with response from a single time point (ΔDAS-3 or ΔDAS-6) as phenotype; all other variables were the same as in the GEE models. Results In the GEE models, borderline significant association was observed at 3 chromosomal regions (6q15: rs284515, p = 6.6x10−7; 6q27: rs75908454, p = 6.3x10−7 and 10q25.3: rs1679568, p = 8.1x10−7), extending to numerous SNPs in linkage disequilibrium (LD) across each region. Potential candidate genes in these regions include MAP3K7, BACH2 (6q15), GFRA1 (10q25.3), and WDR27 (6q27). The association at GFRA1 replicates a previous finding from a Caucasian dataset. In the cross-sectional analyses, ΔDAS-6 was significantly associated with the 6q15 locus (rs284511, p = 2.5x10−8). No other significant or borderline significant associations were identified. Conclusion Three genomic regions demonstrated significant or borderline significant associations with anti-TNF response in our dataset of Japanese RA patients, including a locus previously associated among Caucasians. Using repeated measures of response as phenotype enhanced the power to detect these associations. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-0920-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyoko Honne
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | | | - Chunsen Wu
- Research Unit of Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Obstertics & Gynecology, Odense University Hospital, Odense, Denmark
| | - Ronnie Sebro
- Department of Radiology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Nicholas P Jewell
- School of Public Health, University of California, Berkeley, CA, 94720, USA
| | | | - Masahiro Iwamoto
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Seiji Minota
- Division of Rheumatology and Clinical Immunology, Jichi Medical University, Shimotsuke, Tochigi, Japan
| | - Damini Jawaheer
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.
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