1
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Mack TM, Raddatz MA, Pershad Y, Nachun DC, Taylor KD, Guo X, Shuldiner AR, O'Connell JR, Kenny EE, Loos RJF, Redline S, Cade BE, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Cho MH, DeMeo DL, Levy D, Johnson AD, Mathias RA, Yanek LR, Heckbert SR, Smith NL, Wiggins KL, Raffield LM, Carson AP, Rotter JI, Rich SS, Manichaikul AW, Gu CC, Chen YDI, Lee WJ, Shoemaker MB, Roden DM, Kooperberg C, Auer PL, Desai P, Blackwell TW, Smith AV, Reiner AP, Jaiswal S, Weinstock JS, Bick AG. Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate. NATURE AGING 2024; 4:1043-1052. [PMID: 38834882 DOI: 10.1038/s43587-024-00647-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP), whereby somatic mutations in hematopoietic stem cells confer a selective advantage and drive clonal expansion, not only correlates with age but also confers increased risk of morbidity and mortality. Here, we leverage genetically predicted traits to identify factors that determine CHIP clonal expansion rate. We used the passenger-approximated clonal expansion rate method to quantify the clonal expansion rate for 4,370 individuals in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) cohort and calculated polygenic risk scores for DNA methylation aging, inflammation-related measures and circulating protein levels. Clonal expansion rate was significantly associated with both genetically predicted and measured epigenetic clocks. No associations were identified with inflammation-related lab values or diseases and CHIP expansion rate overall. A proteome-wide search identified predicted circulating levels of myeloid zinc finger 1 and anti-Müllerian hormone as associated with an increased CHIP clonal expansion rate and tissue inhibitor of metalloproteinase 1 and glycine N-methyltransferase as associated with decreased CHIP clonal expansion rate. Together, our findings identify epigenetic and proteomic patterns associated with the rate of hematopoietic clonal expansion.
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Affiliation(s)
- Taralynn M Mack
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael A Raddatz
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Mount Sinai Hospital, New York City, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yii-Der Ida Chen
- Medical Genetics Translational Genomics and Population Sciences (TGPS), Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - M Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas W Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Albert V Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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Zalesak M, Danisovic L, Harsanyi S. Psoriasis and Psoriatic Arthritis-Associated Genes, Cytokines, and Human Leukocyte Antigens. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:815. [PMID: 38792999 PMCID: PMC11123327 DOI: 10.3390/medicina60050815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
In recent years, research has intensified in exploring the genetic basis of psoriasis (PsO) and psoriatic arthritis (PsA). Genome-wide association studies (GWASs), including tools like ImmunoChip, have significantly deepened our understanding of disease mechanisms by pinpointing risk-associated genetic loci. These efforts have elucidated biological pathways involved in PsO pathogenesis, particularly those related to the innate immune system, antigen presentation, and adaptive immune responses. Specific genetic loci, such as TRAF3IP2, REL, and FBXL19, have been identified as having a significant impact on disease development. Interestingly, different genetic variants at the same locus can predispose individuals to either PsO or PsA (e.g., IL23R and deletion of LCE3B and LCE3C), with some variants being uniquely linked to PsA (like HLA B27 on chromosome 6). This article aims to summarize known and new data on the genetics of PsO and PsA, their associated genes, and the involvement of the HLA system and cytokines.
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Affiliation(s)
- Marek Zalesak
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia (L.D.)
| | - Lubos Danisovic
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia (L.D.)
- National Institute of Rheumatic Diseases, Nábrežie Ivana Krasku 4, 921 12 Piestany, Slovakia
| | - Stefan Harsanyi
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 811 08 Bratislava, Slovakia (L.D.)
- National Institute of Rheumatic Diseases, Nábrežie Ivana Krasku 4, 921 12 Piestany, Slovakia
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3
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Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet 2024; 56:838-845. [PMID: 38741015 DOI: 10.1038/s41588-024-01732-8] [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: 09/29/2021] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents determining whether the same allele is responsible, indicating a shared underlying mechanism. Here, using a collection of 129,058 cases and controls across 6 diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles twofold by combining cases and controls across diseases, allowing us to identify more expression quantitative trait loci driven by the shared alleles. The patterns indicate widespread sharing of pathogenic mechanisms but not a single global autoimmune mechanism. Our approach can be applied to any set of traits and is particularly valuable as sample collections become depleted.
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Affiliation(s)
- Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Division of Neurology at the Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Noah Connally
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - David van Heel
- Blizard Institute, Queen Mary University of London, London, UK
| | - Cisca Wijmenga
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leonid Padyukov
- Division of Rheumatology at the Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Robert R Graham
- Maze Therapeutics, South San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Vesalius Therapeutics, Cambridge, MA, USA.
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4
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Cao X, Zhang S, Sha Q. A novel method for multiple phenotype association studies based on genotype and phenotype network. PLoS Genet 2024; 20:e1011245. [PMID: 38728360 PMCID: PMC11111089 DOI: 10.1371/journal.pgen.1011245] [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: 08/18/2023] [Revised: 05/22/2024] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
Joint analysis of multiple correlated phenotypes for genome-wide association studies (GWAS) can identify and interpret pleiotropic loci which are essential to understand pleiotropy in diseases and complex traits. Meanwhile, constructing a network based on associations between phenotypes and genotypes provides a new insight to analyze multiple phenotypes, which can explore whether phenotypes and genotypes might be related to each other at a higher level of cellular and organismal organization. In this paper, we first develop a bipartite signed network by linking phenotypes and genotypes into a Genotype and Phenotype Network (GPN). The GPN can be constructed by a mixture of quantitative and qualitative phenotypes and is applicable to binary phenotypes with extremely unbalanced case-control ratios in large-scale biobank datasets. We then apply a powerful community detection method to partition phenotypes into disjoint network modules based on GPN. Finally, we jointly test the association between multiple phenotypes in a network module and a single nucleotide polymorphism (SNP). Simulations and analyses of 72 complex traits in the UK Biobank show that multiple phenotype association tests based on network modules detected by GPN are much more powerful than those without considering network modules. The newly proposed GPN provides a new insight to investigate the genetic architecture among different types of phenotypes. Multiple phenotypes association studies based on GPN are improved by incorporating the genetic information into the phenotype clustering. Notably, it might broaden the understanding of genetic architecture that exists between diagnoses, genes, and pleiotropy.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
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5
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Schäfer S, Smelik M, Sysoev O, Zhao Y, Eklund D, Lilja S, Gustafsson M, Heyn H, Julia A, Kovács IA, Loscalzo J, Marsal S, Zhang H, Li X, Gawel D, Wang H, Benson M. scDrugPrio: a framework for the analysis of single-cell transcriptomics to address multiple problems in precision medicine in immune-mediated inflammatory diseases. Genome Med 2024; 16:42. [PMID: 38509600 PMCID: PMC10956347 DOI: 10.1186/s13073-024-01314-7] [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: 03/02/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Ineffective drug treatment is a major problem for many patients with immune-mediated inflammatory diseases (IMIDs). Important reasons are the lack of systematic solutions for drug prioritisation and repurposing based on characterisation of the complex and heterogeneous cellular and molecular changes in IMIDs. METHODS Here, we propose a computational framework, scDrugPrio, which constructs network models of inflammatory disease based on single-cell RNA sequencing (scRNA-seq) data. scDrugPrio constructs detailed network models of inflammatory diseases that integrate information on cell type-specific expression changes, altered cellular crosstalk and pharmacological properties for the selection and ranking of thousands of drugs. RESULTS scDrugPrio was developed using a mouse model of antigen-induced arthritis and validated by improved precision/recall for approved drugs, as well as extensive in vitro, in vivo, and in silico studies of drugs that were predicted, but not approved, for the studied diseases. Next, scDrugPrio was applied to multiple sclerosis, Crohn's disease, and psoriatic arthritis, further supporting scDrugPrio through prioritisation of relevant and approved drugs. However, in contrast to the mouse model of arthritis, great interindividual cellular and gene expression differences were found in patients with the same diagnosis. Such differences could explain why some patients did or did not respond to treatment. This explanation was supported by the application of scDrugPrio to scRNA-seq data from eleven individual Crohn's disease patients. The analysis showed great variations in drug predictions between patients, for example, assigning a high rank to anti-TNF treatment in a responder and a low rank in a nonresponder to that treatment. CONCLUSIONS We propose a computational framework, scDrugPrio, for drug prioritisation based on scRNA-seq of IMID disease. Application to individual patients indicates scDrugPrio's potential for personalised network-based drug screening on cellulome-, genome-, and drugome-wide scales. For this purpose, we made scDrugPrio into an easy-to-use R package ( https://github.com/SDTC-CPMed/scDrugPrio ).
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Affiliation(s)
- Samuel Schäfer
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
- Department of Gastroenterology and Hepatology, University Hospital, Linköping, Sweden
| | - Martin Smelik
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | - Oleg Sysoev
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linkoping University, Linköping, Sweden
| | - Yelin Zhao
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | - Desiré Eklund
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - Sandra Lilja
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
- Mavatar, Inc, Stockholm, Sweden
| | - Mika Gustafsson
- Division for Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Antonio Julia
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | - István A Kovács
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, 60208, USA
- Northwestern Institute On Complex Systems, Northwestern University, Evanston, IL, 60208, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Marsal
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | - Huan Zhang
- Centre for Personalised Medicine, Linköping University, Linköping, Sweden
| | - Xinxiu Li
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
| | | | - Hui Wang
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Jiangsu, China
| | - Mikael Benson
- Postal Address: LIME/Medical Digital Twin Research Group, Division of ENT, CLINTEC, Karolinska Institute, Tomtebodavägen 18A. 171 65 Solna, Stockholm, Sweden.
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Aterido A, López-Lasanta M, Blanco F, Juan-Mas A, García-Vivar ML, Erra A, Pérez-García C, Sánchez-Fernández SÁ, Sanmartí R, Fernández-Nebro A, Alperi-López M, Tornero J, Ortiz AM, Fernández-Cid CM, Palau N, Pan W, Byrne-Steele M, Starenki D, Weber D, Rodriguez-Nunez I, Han J, Myers RM, Marsal S, Julià A. Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes. Genome Biol 2024; 25:68. [PMID: 38468286 PMCID: PMC10926600 DOI: 10.1186/s13059-024-03210-0] [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: 03/04/2022] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. RESULTS In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire including reduced diversity as well as altered isotype, chain, and segment frequencies. We demonstrate that therapeutic tumor necrosis factor inhibition partially restores this alteration but find a profound difference in the underlying biochemical reactivities between responders and non-responders. Combining the AIRR with HLA typing, we identify the specific T cell receptor repertoire associated with disease risk variants. Integrating these features, we further develop a molecular classifier that shows the utility of the AIRR as a diagnostic tool. CONCLUSIONS Simultaneous sequencing of the seven chains of the human AIRR reveals novel features associated with the disease and clinically relevant phenotypes, including response to therapy. These findings show the unique potential of AIRR to address precision medicine in immune-related diseases.
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Affiliation(s)
- Adrià Aterido
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Francisco Blanco
- Rheumatology Department, Hospital Juan Canalejo, A Coruña, Spain
| | | | | | - Alba Erra
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
- Rheumatology Department, Hospital Sant Rafael, Barcelona, Spain
| | | | | | - Raimon Sanmartí
- Rheumatology Department, Hospital Clínic de Barcelona and IDIBAPS, Barcelona, Spain
| | | | | | - Jesús Tornero
- Rheumatology Department, Hospital Universitario Guadalajara, Guadalajara, Spain
| | - Ana María Ortiz
- Rheumatology Department, Hospital Universitario La Princesa, IIS La Princesa, Madrid, Spain
| | | | - Núria Palau
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | | | | | | | | | | | - Jian Han
- iRepertoire Inc, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sara Marsal
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall Hebron Research Institute, 08035, Barcelona, Spain.
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7
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Cao X, Liang X, Zhang S, Sha Q. Gene selection by incorporating genetic networks into case-control association studies. Eur J Hum Genet 2024; 32:270-277. [PMID: 36529820 PMCID: PMC10923938 DOI: 10.1038/s41431-022-01264-x] [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: 04/08/2022] [Revised: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Large-scale genome-wide association studies (GWAS) have been successfully applied to a wide range of genetic variants underlying complex diseases. The network-based regression approach has been developed to incorporate a biological genetic network and to overcome the challenges caused by the computational efficiency for analyzing high-dimensional genomic data. In this paper, we propose a gene selection approach by incorporating genetic networks into case-control association studies for DNA sequence data or DNA methylation data. Instead of using traditional dimension reduction techniques such as principal component analyses and supervised principal component analyses, we use a linear combination of genotypes at SNPs or methylation values at CpG sites in a gene to capture gene-level signals. We employ three linear combination approaches: optimally weighted sum (OWS), beta-based weighted sum (BWS), and LD-adjusted polygenic risk score (LD-PRS). OWS and LD-PRS are supervised approaches that depend on the effect of each SNP or CpG site on the case-control status, while BWS can be extracted without using the case-control status. After using one of the linear combinations of genotypes or methylation values in each gene to capture gene-level signals, we regularize them to perform gene selection based on the biological network. Simulation studies show that the proposed approaches have higher true positive rates than using traditional dimension reduction techniques. We also apply our approaches to DNA methylation data and UK Biobank DNA sequence data for analyzing rheumatoid arthritis. The results show that the proposed methods can select potentially rheumatoid arthritis related genes that are missed by existing methods.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
| | - Xiaoyu Liang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, USA.
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8
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Xu X, Wu LY, Wang SY, Yan M, Wang YH, Li L, Sun ZL, Zhao JX. Investigating causal associations among gut microbiota, metabolites, and psoriatic arthritis: a Mendelian randomization study. Front Microbiol 2024; 15:1287637. [PMID: 38426052 PMCID: PMC10902440 DOI: 10.3389/fmicb.2024.1287637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Background Currently, there has been observed a significant alteration in the composition of the gut microbiome (GM) and serum metabolites in patients with psoriatic arthritis (PsA) compared to healthy individuals. However, previous observational studies have shown inconsistent results regarding the alteration of gut microbiota/metabolites. In order to shed light on this matter, we utilized Mendelian randomization to determine the causal effect of GM/metabolites on PsA. Methods We retrieved summary-level data of GM taxa/metabolites and PsA from publicly available GWAS statistics. Causal relationships between GM/metabolites and PsA were determined using a two-sample MR analysis, with the IVW approach serving as the primary analysis method. To ensure the robustness of our findings, we conducted sensitivity analyses, multivariable MR analysis (MVMR), and additional analysis including replication verification analysis, LDSC regression, and Steiger test analysis. Furthermore, we investigated reverse causality through a reverse MR analysis. Finally, we conducted an analysis of expression quantitative trait loci (eQTLs) involved in the metabolic pathway to explore potential molecular mechanisms of metabolism. Results Our findings reveal that eight GM taxa and twenty-three serum metabolites are causally related to PsA (P < 0.05). Notably, a higher relative abundance of Family Rikenellaceae (ORIVW: 0.622, 95% CI: 0.438-0.883, FDR = 0.045) and elevated serum levels of X-11538 (ORIVW: 0.442, 95% CI: 0.250-0.781, FDR = 0.046) maintain significant causal associations with a reduced risk of PsA, even after adjusting for multiple testing correction and conducting MVMR analysis. These findings suggest that Family Rikenellaceae and X-11538 may have protective effects against PsA. Our sensitivity analysis and additional analysis revealed no significant horizontal pleiotropy, reverse causality, or heterogeneity. The functional enrichment analysis revealed that the eQTLs examined were primarily associated with glycerolipid metabolism and the expression of key metabolic factors influenced by bacterial infections (Vibrio cholerae and Helicobacter pylori) as well as the mTOR signaling pathway. Conclusion In conclusion, our study demonstrates that Family Rikenellaceae and X-11538 exhibit a strong and negative causal relationship with PsA. These particular GM taxa and metabolites have the potential to serve as innovative biomarkers, offering valuable insights into the treatment and prevention of PsA. Moreover, bacterial infections and mTOR-mediated activation of metabolic factors may play an important role in this process.
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Affiliation(s)
- Xiao Xu
- Department of Nursing, Nantong Health College of Jiangsu Province, Nantong, China
| | - Lin-yun Wu
- School of Nursing, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shu-yun Wang
- Academic Affair Office, Nantong Vocational University, Nantong, China
| | - Min Yan
- Department of Epidemiology, School of Public Health, Changzhou University, Changzhou, China
- Faculty of Health and Welfare, Satakunta University of Applied Sciences, Pori, Finland
| | - Yuan-Hong Wang
- Department of Rheumatology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Li Li
- Department of Rheumatology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi-ling Sun
- Department of Epidemiology, School of Public Health, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ji-Xiang Zhao
- Department of Nursing, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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9
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Schäfer S, Smelik M, Sysoev O, Zhao Y, Eklund D, Lilja S, Gustafsson M, Heyn H, Julia A, Kovács IA, Loscalzo J, Marsal S, Zhang H, Li X, Gawel D, Wang H, Benson M. scDrugPrio: A framework for the analysis of single-cell transcriptomics to address multiple problems in precision medicine in immune-mediated inflammatory diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566249. [PMID: 38014022 PMCID: PMC10680570 DOI: 10.1101/2023.11.08.566249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background Ineffective drug treatment is a major problem for many patients with immune-mediated inflammatory diseases (IMIDs). Important reasons are the lack of systematic solutions for drug prioritisation and repurposing based on characterisation of the complex and heterogeneous cellular and molecular changes in IMIDs. Methods Here, we propose a computational framework, scDrugPrio, which constructs network models of inflammatory disease based on single-cell RNA sequencing (scRNA-seq) data. scDrugPrio constructs detailed network models of inflammatory diseases that integrate information on cell type-specific expression changes, altered cellular crosstalk and pharmacological properties for the selection and ranking of thousands of drugs. Results scDrugPrio was developed using a mouse model of antigen-induced arthritis and validated by improved precision/recall for approved drugs, as well as extensive in vitro, in vivo, and in silico studies of drugs that were predicted, but not approved, for the studied diseases. Next, scDrugPrio was applied to multiple sclerosis, Crohn's disease, and psoriatic arthritis, further supporting scDrugPrio through prioritisation of relevant and approved drugs. However, in contrast to the mouse model of arthritis, great interindividual cellular and gene expression differences were found in patients with the same diagnosis. Such differences could explain why some patients did or did not respond to treatment. This explanation was supported by the application of scDrugPrio to scRNA-seq data from eleven individual Crohn's disease patients. The analysis showed great variations in drug predictions between patients, for example, assigning a high rank to anti-TNF treatment in a responder and a low rank in a nonresponder to that treatment. Conclusion We propose a computational framework, scDrugPrio, for drug prioritisation based on scRNA-seq of IMID disease. Application to individual patients indicates scDrugPrio's potential for personalised network-based drug screening on cellulome-, genome-, and drugome-wide scales. For this purpose, we made scDrugPrio into an easy-to-use R package (https://github.com/SDTC-CPMed/scDrugPrio).
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Affiliation(s)
- Samuel Schäfer
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Department of Gastroenterology and Hepatology, University Hospital, Linköping, Sweden
| | - Martin Smelik
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Oleg Sysoev
- Division of Statistics and Machine Learning, Department of Computer and Information Science, Linkoping University; Linköping, Sweden
| | - Yelin Zhao
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Desiré Eklund
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
| | - Sandra Lilja
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Mavatar, Inc., Stockholm. Sweden
| | - Mika Gustafsson
- Division for Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University; Linköping, Sweden
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Antonio Julia
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d’Hebron, Barcelona, España
| | - István A. Kovács
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | - Sara Marsal
- Grup de Recerca de Reumatologia, Institut de Recerca Vall d’Hebron, Barcelona, España
| | - Huan Zhang
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
| | - Xinxiu Li
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
| | - Danuta Gawel
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Mavatar, Inc., Stockholm. Sweden
| | - Hui Wang
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208, USA
| | - Mikael Benson
- Centre for Personalised Medicine, Linköping University; Linköping, Sweden
- Division of ENT, CLINTEC, Karolinska Institute, Stockholm, Sweden
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10
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Parperis K, Kyriakou A, Voskarides K, Koliou E, Evangelou M, Chatzittofis A. Insights into suicidal behavior among psoriatic arthritis patients: A systematic review and a genetic linkage disequilibrium analysis. Semin Arthritis Rheum 2023; 62:152241. [PMID: 37429140 DOI: 10.1016/j.semarthrit.2023.152241] [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: 01/09/2023] [Revised: 06/15/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023]
Abstract
OBJECTIVES To systematically assess the magnitude of suicidal behavior among PsA patients and identify associated risk factors. Also identify common genes or coinherited single nucleotide polymorphisms (SNPs) implicated in suicidal behavior and PsA. METHODS Based on the PRISMA guidelines, we conducted a systematic literature review of the online databases PubMed/Medline, Web of Science, and EMBASE from inception to May 2022. Full-text original articles that describe suicidal behavior in PsA patients were eligible. All registered genome-wide association study (GWAS) data in the GWAS catalog database for PsA and psychiatric traits, such as suicidal behavior, and depression, were downloaded for further analysis. RESULTS A total of 48 articles were identified, and 6 were relevant to the study question .Among the 122,160 PsA patients, 700 had suicidal behavior (0,57%). The range of age in one study was between 30 and 49 years, and 64% of PsA patients with suicidal behavior were female. Among 13,899 PsA patients 74 had suicidal ideation (0.53%) and 125 suicide attempts occurred (0.9%). In two studies, among 17,383 patients, 13 complete suicides occurred (0.07%). A genetic haplotype on chromosomal region 6p21.1, spanning from 29,597,596 to 32,251,264 Mb, contains predisposing SNPs for PsA and depression. 6p21.1-6p21.3 is the chromosomal region containing the HLA genes of classes I, II and III. CONCLUSION Suicide behavior in PsA patients was associated with depression and other psychiatric comorbidities. Further evidence supports a genetic origin, at least partly. Awareness of these findings can help clinicians to recognize suicide behavior and prevent suicide attempts.
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Affiliation(s)
- Konstantinos Parperis
- Division of Rheumatology, Department of Medicine, University of Cyprus Medical School, Nicosia, Cyprus
| | - Avgoustina Kyriakou
- Internal Medicine Resident Larnaca General Hospital, Department of Medicine, University of Cyprus Medical School, Nicosia, Cyprus.
| | - Konstantinos Voskarides
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia, Cyprus; School of Veterinary Medicine, University of Nicosia, Nicosia, Cyprus
| | - Eleni Koliou
- Department of Medicine, University of Cyprus Medical School, Nicosia, Cyprus
| | - Marina Evangelou
- Department of Medicine, University of Cyprus Medical School, Nicosia, Cyprus
| | - Andreas Chatzittofis
- Department of Psychiatry, University of Cyprus Medical School, Nicosia, Cyprus and Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden
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11
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Soomro M, Hum R, Barton A, Bowes J. Genetic Studies Investigating Susceptibility to Psoriatic Arthritis: A Narrative Review. Clin Ther 2023; 45:810-815. [PMID: 37516563 DOI: 10.1016/j.clinthera.2023.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/31/2023]
Abstract
PURPOSE Approximately 30% of patients with psoriasis will develop psoriatic arthritis (PsA), leading to a decreased quality of life for the patient caused by increasing disability and additional health complications. The identification of risk factors for the development of PsA would facilitate the development of risk prediction models in which patients with psoriasis at high risk of developing PsA could be targeted in a stratified medicine approach, enabling early intervention and treatment. PsA is known to have a genetic contribution to susceptibility, and the identification of genetic risk factors that differentiate PsA from cutaneous-only psoriasis is a key area of research. This narrative review summarizes the discovery of genetic risk factors and, with the aid of a primer on risk prediction models, discusses their potential role for the classification of PsA risk and diagnosis. METHODS All relevant research articles were identified through searches of the PubMed database for literature published up until December 2022. Search terms included psoriatic arthritis, genetic susceptibility, genetic association, genome-wide association study, GWAS, prediction, and polygenic risk score. FINDINGS The current literature reveals considerable overlap between the genetic susceptibility loci for PsA and psoriasis. Several PsA-specific genetic risk factors have been reported, and most notably these implicate the HLA-B and IL23R genes. Efforts to include genetic risk factors in prediction models for the development of PsA have reported good discrimination. IMPLICATIONS Key messages emerging from this narrative are as follows: the limited number of PsA-specific susceptibility loci reported to date suggest larger studies are required, facilitated by international collaboration, to achieve the power to detect further genetic factors; the early promising results for genetic-based risk prediction require further validation in independent datasets; and risk prediction models combining clinical and genetic risk factors have yet to be explored.
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Affiliation(s)
- Mehreen Soomro
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Ryan Hum
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom; NIHR Manchester Biomedical Research Centre, Central Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom; NIHR Manchester Biomedical Research Centre, Central Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom.
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12
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Hüffmeier U, Klima J, Hayatu MD. Genetic underpinnings of the psoriatic spectrum. MED GENET-BERLIN 2023; 35:46-54. [PMID: 38835412 PMCID: PMC10842586 DOI: 10.1515/medgen-2023-2005] [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: 06/06/2024]
Abstract
The psoriatic field includes both rare and common subtypes. Common complex forms include psoriasis vulgaris and psoriatic arthritis. In these subtypes, certain HLA alleles remain the most relevant genetic factors, although genome-wide association studies lead to the detection of more than 80 susceptibility loci. They mainly affect innate and adaptive immunity and explain over 28 % of the heritability. Pustular psoriasis comprises a group of rarer subtypes. Using exome sequencing, several disease genes were identified for mainly generalized pustular psoriasis, and an oligogenic inheritance is likely. Treatment studies based on the affected IL-36 pathway indicate a high response rate in this subtype further supporting the pathophysiological relevance of the affected gene products.
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Affiliation(s)
- Ulrike Hüffmeier
- Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Institute of Human Genetics Schwabachanlage 10 91054 Erlangen Deutschland
| | - Janine Klima
- Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Institute of Human Genetics Schwabachanlage 10 91054 Erlangen Germany
| | - Mohammad Deen Hayatu
- Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Institute of Human Genetics Schwabachanlage 10 91054 Erlangen Germany
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13
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Michelena X, López-Medina C, Erra A, Juanola X, Font-Ugalde P, Collantes E, Marzo-Ortega H. Characterising the axial phenotype of psoriatic arthritis: a study comparing axial psoriatic arthritis and ankylosing spondylitis with psoriasis from the REGISPONSER registry. RMD Open 2022; 8:rmdopen-2022-002513. [PMID: 36597989 PMCID: PMC9723956 DOI: 10.1136/rmdopen-2022-002513] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
AIMS To explore the clinical and radiographical characteristics of axial psoriatic arthritis (PsA) and to compare it with ankylosing spondylitis (AS) with psoriasis. METHODS Cross-sectional study from the national multicentre registry REGISPONSER where participants fulfilled the European Spondyloarthropathy Study Group spondyloarthritis criteria at entry. Clinical, laboratory and radiographical characteristics between patients classified as axial PsA and AS with psoriasis by their rheumatologist are compared according to HLA-B27 status. RESULTS Of 2367 patients on REGISPONSER, n=405 had PsA, of whom 27% (n=109) had axial involvement as per the treating rheumatologist. 30% (n=26/86) of axial PsA were HLA-B27 positive. In the AS group, 9% (127/1422) had a history of psoriasis and were more frequently male, with longer diagnostic delay and more anterior uveitis than those with axial PsA who had more peripheral involvement and nail disease. Patients with HLA-B27-negative axial PsA reported less inflammatory pain and structural damage compared with AS with psoriasis. By contrast, HLA-B27-positive axial PsA shared clinical characteristics similar to AS and psoriasis although with a lower BASRI score. In the multivariable analysis, patients with AS and psoriasis were independently associated with HLA-B27 positivity (OR 3.34, 95% CI 1.42 to 7.85) and lumbar structural damage scored by BASRI (OR 2.14, 95% CI 1.4 to 3.19). CONCLUSION The more prevalent axial PsA phenotype is predominantly HLA-B27 negative and presents different clinical and radiological manifestations when compared with AS with psoriasis. There is great heterogeneity in what rheumatologists consider axial PsA from a clinical and imaging perspective, highlighting the need for research into possible genetic drivers and a consensus definition.
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Affiliation(s)
- Xabier Michelena
- Rheumatology, Hospital Universitari Vall d'Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain,NIHR Leeds BRC, Leeds Teaching Hospitals Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Clementina López-Medina
- Maimónides Institute for Biomedical Research of Córdoba (IMIBIC), Córdoba, Spain,Rheumatology, Reina Sofía University Hospital, Córdoba, Spain
| | - Alba Erra
- Rheumatology, Hospital Universitari Vall d'Hebron, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Xavier Juanola
- Rheumatology, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Pilar Font-Ugalde
- Maimónides Institute for Biomedical Research of Córdoba (IMIBIC), Córdoba, Spain,Rheumatology, Reina Sofía University Hospital, Córdoba, Spain
| | - Eduardo Collantes
- Maimónides Institute for Biomedical Research of Córdoba (IMIBIC), Córdoba, Spain,Rheumatology, Reina Sofía University Hospital, Córdoba, Spain
| | - Helena Marzo-Ortega
- NIHR Leeds BRC, Leeds Teaching Hospitals Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
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14
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Julià A, Gómez A, López-Lasanta M, Blanco F, Erra A, Fernández-Nebro A, Mas AJ, Pérez-García C, Vivar MLG, Sánchez-Fernández S, Alperi-López M, Sanmartí R, Ortiz AM, Fernandez-Cid CM, Díaz-Torné C, Moreno E, Li T, Martínez-Mateu SH, Absher DM, Myers RM, Molina JT, Marsal S. Longitudinal analysis of blood DNA methylation identifies mechanisms of response to tumor necrosis factor inhibitor therapy in rheumatoid arthritis. EBioMedicine 2022; 80:104053. [PMID: 35576644 PMCID: PMC9118662 DOI: 10.1016/j.ebiom.2022.104053] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 11/07/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic, immune-mediated inflammatory disease of the joints that has been associated with variation in the peripheral blood methylome. In this study, we aim to identify epigenetic variation that is associated with the response to tumor necrosis factor inhibitor (TNFi) therapy. Methods Peripheral blood genome-wide DNA methylation profiles were analyzed in a discovery cohort of 62 RA patients at baseline and at week 12 of TNFi therapy. DNA methylation of individual CpG sites and enrichment of biological pathways were evaluated for their association with drug response. Using a novel cell deconvolution approach, altered DNA methylation associated with TNFi response was also tested in the six main immune cell types in blood. Validation of the results was performed in an independent longitudinal cohort of 60 RA patients. Findings Treatment with TNFi was associated with significant longitudinal peripheral blood methylation changes in biological pathways related to RA (FDR<0.05). 139 biological functions were modified by therapy, with methylation levels changing systematically towards a signature similar to that of healthy controls. Differences in the methylation profile of T cell activation and differentiation, GTPase-mediated signaling, and actin filament organization pathways were associated with the clinical response to therapy. Cell type deconvolution analysis identified CpG sites in CD4+T, NK, neutrophils and monocytes that were significantly associated with the response to TNFi. Interpretation Our results show that treatment with TNFi restores homeostatic blood methylation in RA. The clinical response to TNFi is associated to methylation variation in specific biological pathways, and it involves cells from both the innate and adaptive immune systems. Funding The Instituto de Salud Carlos III.
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Affiliation(s)
- Antonio Julià
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain.
| | - Antonio Gómez
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain
| | - María López-Lasanta
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain
| | - Francisco Blanco
- Rheumatology Department, INIBIC-Hospital Universitario A Coruña, A Coruña, Spain
| | - Alba Erra
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain; Rheumatology Department, Hospital de San Rafael, Barcelona, Spain
| | | | - Antonio Juan Mas
- Rheumatology Department, Hospital Universitario Son Llàtzer, Mallorca, Spain
| | | | | | | | | | - Raimon Sanmartí
- Rheumatology Department, Fundació Clínic Recerca Biomèdica, Barcelona, Spain
| | - Ana María Ortiz
- Rheumatology Department, Hospital Universitario La Princesa, Madrid, Spain
| | | | - César Díaz-Torné
- Rheumatology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Estefania Moreno
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain; Rheumatology Unit, Consorci Sanitari de l'Alt Penedès, Spain
| | - Tianlu Li
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain
| | - Sergio H Martínez-Mateu
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | | | - Sara Marsal
- Rheumatology Research Group, Vall d'Hebron University Hospital Research Institute, Barcelona 08035, Spain.
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15
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Soomro M, Stadler M, Dand N, Bluett J, Jadon D, Jalali-Najafabadi F, Duckworth M, Ho P, Marzo-Ortega H, Helliwell PS, Ryan AW, Kane D, Korendowych E, Simpson MA, Packham J, McManus R, Gabay C, Lamacchia C, Nissen MJ, Brown MA, Verstappen SMM, Van Staa T, Barker JN, Smith CH, FitzGerald O, McHugh N, Warren RB, Bowes J, Barton A. Comparative genetic analysis of psoriatic arthritis and psoriasis for the discovery of genetic risk factors and risk prediction modelling. Arthritis Rheumatol 2022; 74:1535-1543. [PMID: 35507331 PMCID: PMC9539852 DOI: 10.1002/art.42154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/16/2022] [Accepted: 04/28/2022] [Indexed: 11/10/2022]
Abstract
Objectives Psoriatic arthritis (PsA) has a strong genetic component, and the identification of genetic risk factors could help identify the ~30% of psoriasis patients at high risk of developing PsA. Our objectives were to identify genetic risk factors and pathways that differentiate PsA from cutaneous‐only psoriasis (PsC) and to evaluate the performance of PsA risk prediction models. Methods Genome‐wide meta‐analyses were conducted separately for 5,065 patients with PsA and 21,286 healthy controls and separately for 4,340 patients with PsA and 6,431 patients with PsC. The heritability of PsA was calculated as a single‐nucleotide polymorphism (SNP)–based heritability estimate (h2SNP) and biologic pathways that differentiate PsA from PsC were identified using Priority Index software. The generalizability of previously published PsA risk prediction pipelines was explored, and a risk prediction model was developed with external validation. Results We identified a novel genome‐wide significant susceptibility locus for the development of PsA on chromosome 22q11 (rs5754467; P = 1.61 × 10−9), and key pathways that differentiate PsA from PsC, including NF‐κB signaling (adjusted P = 1.4 × 10−45) and Wnt signaling (adjusted P = 9.5 × 10−58). The heritability of PsA in this cohort was found to be moderate (h2SNP = 0.63), which was similar to the heritability of PsC (h2SNP = 0.61). We observed modest performance of published classification pipelines (maximum area under the curve 0.61), with similar performance of a risk model derived using the current data. Conclusion Key biologic pathways associated with the development of PsA were identified, but the investigation of risk classification revealed modest utility in the available data sets, possibly because many of the PsC patients included in the present study were receiving treatments that are also effective in PsA. Future predictive models of PsA should be tested in PsC patients recruited from primary care.
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Affiliation(s)
- Mehreen Soomro
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - Michael Stadler
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - Nick Dand
- Department of Medical and Molecular Genetics, School of Basic & Medical Biosciences, King's College London, London, UK
| | - James Bluett
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK
| | - Deepak Jadon
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Farideh Jalali-Najafabadi
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - Michael Duckworth
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Pauline Ho
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK
| | - Helena Marzo-Ortega
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Philip S Helliwell
- NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Anthony W Ryan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland.,Genuity Science, Cherrywood Business Park, Dublin, Ireland
| | - David Kane
- Tallaght University Hospital and Trinity College Dublin, Ireland
| | - Eleanor Korendowych
- Royal National Hospital for Rheumatic Diseases and Dept Pharmacy and Pharmacology, University of Bath, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, School of Basic & Medical Biosciences, King's College London, London, UK
| | - Jonathan Packham
- Rheumatology Department, Haywood Hospital, Stoke on Trent, Midlands Partnership NHS Foundation Trust, UK.,Academic Unit of Population and Lifespan Sciences, University of Nottingham, University of Nottingham, UK
| | - Ross McManus
- Department of Clinical Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Cem Gabay
- Division of Rheumatology, Department of Medicine, Geneva University Hospitals & Department of Pathology and Immunology, University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Céline Lamacchia
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Michael J Nissen
- Division of Rheumatology, Geneva University Hospital, Geneva, Switzerland
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Genomics England, Charterhouse Square, London, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK.,Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Tjeerd Van Staa
- Health e-Research Centre, Health Data Research UK North, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, Manchester, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Guys and St Thomas' Foundation Trust and Kings College London, London, UK
| | | | | | - Oliver FitzGerald
- UCD School of Medicine and Medical Sciences and Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland
| | - Neil McHugh
- Royal National Hospital for Rheumatic Diseases and Dept Pharmacy and Pharmacology, University of Bath, UK
| | - Richard B Warren
- Dermatology Centre, Salford Royal NHS Foundation Trust, Manchester NIHR Biomedical Research Centre, University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, UK
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16
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Laborde CM, Larzabal L, González-Cantero Á, Castro-Santos P, Díaz-Peña R. Advances of Genomic Medicine in Psoriatic Arthritis. J Pers Med 2022; 12:jpm12010035. [PMID: 35055350 PMCID: PMC8780979 DOI: 10.3390/jpm12010035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Psoriatic arthritis (PsA) is a common type of inflammatory arthritis found in up to 40% of patients with psoriasis. Although early diagnosis is important for reducing the risk of irreversible structural damage, there are no adequate screening tools for this purpose, and there are no clear markers of predisposition to the disease. Much evidence indicates that PsA disorder is complex and heterogeneous, where genetic and environmental factors converge to trigger inflammatory events and the development of the disease. Nevertheless, the etiologic events that underlie PsA are complex and not completely understood. In this review, we describe the existing data in PsA in order to highlight the need for further research in this disease to progress in the knowledge of its pathobiology and to obtain early diagnosis tools for these patients.
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Affiliation(s)
| | | | - Álvaro González-Cantero
- Department of Dermatology, Hospital Universitario Ramon y Cajal, 28034 Madrid, Spain;
- Faculty of Medicine, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda, 28223 Pozuelo de Alarcón, 28034 Madrid, Spain
| | - Patricia Castro-Santos
- Immunology, Centro de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, 36310 Vigo, Spain;
| | - Roberto Díaz-Peña
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca 3460000, Chile
- Correspondence: or ; Tel.: +34-981-955-073
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17
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Gao J, Shen X, Ko R, Huang C, Shen C. Cognitive Process of Psoriasis and Its Comorbidities: From Epidemiology to Genetics. Front Genet 2021; 12:735124. [PMID: 34899832 PMCID: PMC8662384 DOI: 10.3389/fgene.2021.735124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
Psoriasis (PsO) is a chronic inflammatory skin disease that affects approximately 2% of the population all over the world. Comorbidities of PsO have increasingly garnered more interest in the past decades. Compared with the normal population, the incidences of comorbidities are higher among patients with PsO. In the last 20 years, researchers have focused on studying the genetic components of PsO, and genetic associations between PsO and its comorbidities were elucidated. This review provides an in-depth understanding and summarization of the connection between PsO and its comorbidities from the perspectives of epidemiology and genetics. Further understanding of PsO and its comorbidities will promote research on the pathogenesis, drug development, novel therapy methods, and personalized and precision treatment of PsO and its comorbidities.
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Affiliation(s)
- Jing Gao
- Department of Dermatology, the Second Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Xue Shen
- Department of Dermatology, Chengdu Second People’s Hospital, Chengdu, China
| | - Randy Ko
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Cong Huang
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University–the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Changbing Shen
- Department of Dermatology, Peking University Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory for Translational Medicine of Dermatology, Shenzhen Peking University–the Hong Kong University of Science and Technology Medical Center, Shenzhen, China
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18
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Kubanov AA, Karamova AE, Chikin VV, Verbenko DA, Znamenskaya LF, Artamonova OG. Genetic markers for psoriatic arthritis in patients with psoriasis. Part I: non-HLA genes. VESTNIK DERMATOLOGII I VENEROLOGII 2021. [DOI: 10.25208/vdv1260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Psoriatic arthritis often develops in patients with psoriasis and can lead to joint deformity, stiffness, dysfunction, and disability. Psoriatic arthritis is a polygenic disease. and the issue of personalizing the prognosis of its development can only be resolved taking into account the variability of plenty genomic loci associated with the development of the disease. The personification of the prognosis of the disease can be solved taking into account the variability of the set of genomic loci with which its development is associated. The review examines genomic polymorphisms associated with the development of psoriatic arthritis not psoriasis, except of HLA polymorphisms. Genome regions containing polymorphisms, allelic variants of which are associated both with the development of psoriatic arthritis and reducing the likelihood of its occurrence, are described. It has been reported that the predisposition to the development of psoriatic arthritis in patients with psoriasis is determined by genes encoding proteins involved in inflammation and bone metabolism.
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19
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Wang CM, Jan Wu YJ, Lin JC, Huang LY, Wu J, Chen JY. Genetic effects of B3GNT2 on ankylosing spondylitis susceptibility and clinical manifestations in Taiwanese. J Formos Med Assoc 2021; 121:1283-1294. [PMID: 34645591 DOI: 10.1016/j.jfma.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/09/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND/PURPOSE The intergenic SNP rs10865331 at 2p15 was identified as a major risk factor for ankylosing spondylitis (AS) susceptibility in genome-wide association studies (GWAS). B3GNT2 gene regulates polylactosamine synthesis is potentially functionally relevant to AS disease development. We investigated whether SNP rs10865331 and two B3GNT2 SNPs (rs11900673 and rs1136151) are associated with AS susceptibility and disease severity in Taiwanese. METHODS Distributions of genotypes, alleles, and haplotypes of three SNPs were compared between 1,472 AS patients and 2,117 healthy blood donors and among AS patients stratified by clinical characteristics. RESULTS The intergenic SNP rs10865331 was significantly associated with AS (PFDR = 1.02E-05) in Taiwanese. In AS patients stratified by positivity of HLA-B27 and syndesmophyte formation, all three B3GNT2 locus SNPs (rs11900673, rs1136151, and rs10865331) were significantly associated with syndesmophyte formation among HLA-B27 positive AS patients. Haplotype analyses revealed that the "CTA" (rs11900673C/rs1136151T/rs10865331A) haplotype was significantly associated with AS susceptibility (Padj = 0.0177) and syndesmophyte formation (Padj = 0.016) in HLA-B27 positive patients. In contrast, "TCG" (rs11900673T/rs1136151C/rs10865331G) haplotype showed protection against AS development (Padj = 0.0005 for HLA-B27 positive and Padj = 0.004 for HLA-B27 negative, respectively) and syndesmophyte formation (Padj = 0.0017) in HLA-B27 positive patients. Furthermore, B3GNT2 mRNA expressions were negatively associated with erythrocyte sedimentation rate (ESR, P = 0.0103), C-reactive protein (CRP, P = 0.0353), Bath ankylosing spondylitis functional index (BASFI, P = 0.0171), and syndesmophyte formation (P = 0.0148). CONCLUSION Our data suggest that B3GNT2 gene may contribute to AS development and affect AS severity by interacting with HLA-B27 in Taiwanese.
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Affiliation(s)
- Chin-Man Wang
- Department of Physical Medicine Rehabilitation, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan
| | - Yeong-Jian Jan Wu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan
| | - Jing-Chi Lin
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan
| | - Li-Yu Huang
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan
| | - Jianming Wu
- Dept. of Veterinary and Biomedical Sciences, Dept. of Medicine, University of Minnesota, USA
| | - Ji-Yih Chen
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan.
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20
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Grivas A, Fragoulis G, Garantziotis P, Banos A, Nikiphorou E, Boumpas D. Unraveling the complexities of psoriatic arthritis by the use of -Omics and their relevance for clinical care. Autoimmun Rev 2021; 20:102949. [PMID: 34509654 DOI: 10.1016/j.autrev.2021.102949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 12/30/2022]
Abstract
-Omic technologies represent a novel approach to unravel ill-defined aspects of psoriatic arthritis (PsA). Large-scale information can be acquired from analysis of affected tissues in PsA via high-throughput studies in the domains of genomics, transcriptomics, epigenetics, proteomics and metabolomics. This is a critical overview of the current knowledge of -omics in PsA, with emphasis on the pathophysiological insights of diagnostic and therapeutic relevance, the advent of novel biomarkers and their potential use for precision medicine in PsA.
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Affiliation(s)
- Alexandros Grivas
- National and Kapodistrian University of Athens, Faculty of medicine, Athens, Greece; Inflammation & Autoimmunity Lab, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.
| | - George Fragoulis
- First Department of Propaedeutic Internal Medicine, National and Kapodistrian University of Athens, "Laiko" General Hospital, Athens, Greece
| | - Panagiotis Garantziotis
- Inflammation & Autoimmunity Lab, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece; Division of Immunology and Rheumatology, Hannover Medical University, 30,625 Hannover, Germany
| | - Aggelos Banos
- Inflammation & Autoimmunity Lab, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Elena Nikiphorou
- Centre for Rheumatic Diseases, School of Immunology and Microbial Sciences, King's College London, King's Hospital, London, United Kingdom
| | - Dimitrios Boumpas
- National and Kapodistrian University of Athens, Faculty of medicine, Athens, Greece; Inflammation & Autoimmunity Lab, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
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21
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Ruggiero D, Nutile T, Nappo S, Tirozzi A, Bellenguez C, Leutenegger AL, Ciullo M. Genetics of PlGF plasma levels highlights a role of its receptors and supports the link between angiogenesis and immunity. Sci Rep 2021; 11:16821. [PMID: 34413389 PMCID: PMC8376970 DOI: 10.1038/s41598-021-96256-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022] Open
Abstract
Placental growth factor (PlGF) is a member of the vascular endothelial growth factor family and is involved in bone marrow-derived cell activation, endothelial stimulation and pathological angiogenesis. High levels of PlGF have been observed in several pathological conditions especially in cancer, cardiovascular, autoimmune and inflammatory diseases. Little is known about the genetics of circulating PlGF levels. Indeed, although the heritability of circulating PlGF levels is around 40%, no studies have assessed the relation between PlGF plasma levels and genetic variants at a genome-wide level. In the current study, PlGF plasma levels were measured in a population-based sample of 2085 adult individuals from three isolated populations of South Italy. A GWAS was performed in a discovery cohort (N = 1600), followed by a de novo replication (N = 468) from the same populations. The meta-analysis of the discovery and replication samples revealed one signal significantly associated with PlGF circulating levels. This signal was mapped to the PlGF co-receptor coding gene NRP1, indicating its important role in modulating the PlGF plasma levels. Two additional signals, at the PlGF receptor coding gene FLT1 and RAPGEF5 gene, were identified at a suggestive level. Pathway and TWAS analyses highlighted genes known to be involved in angiogenesis and immune response, supporting the link between these processes and PlGF regulation. Overall, these data improve our understanding of the genetic variation underlying circulating PlGF levels. This in turn could lead to new preventive and therapeutic strategies for a wide variety of PlGF-related pathologies.
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Affiliation(s)
- Daniela Ruggiero
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", National Research Council of Italy (CNR), Via Pietro Castellino, 111, 80131, Naples, Italy.
- IRCCS Neuromed, Pozzilli, Isernia, Italy.
| | - Teresa Nutile
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", National Research Council of Italy (CNR), Via Pietro Castellino, 111, 80131, Naples, Italy
| | | | | | - Celine Bellenguez
- CHU Lille, U1167 - Labex DISTALZ - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Inserm, Institut Pasteur de Lille, Univ. Lille, 59000, Lille, France
| | - Anne-Louise Leutenegger
- UMR 946, Genetic Variation and Human Diseases, Inserm, 75010, Paris, France
- UMR946, Université Paris-Diderot, Sorbonne Paris Cité, 75010, Paris, France
| | - Marina Ciullo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", National Research Council of Italy (CNR), Via Pietro Castellino, 111, 80131, Naples, Italy.
- IRCCS Neuromed, Pozzilli, Isernia, Italy.
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22
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Mulder MLM, van Hal TW, Wenink MH, Koenen HJPM, van den Hoogen FHJ, de Jong EMGJ, van den Reek JMPA, Vriezekolk JE. Clinical, laboratory, and genetic markers for the development or presence of psoriatic arthritis in psoriasis patients: a systematic review. Arthritis Res Ther 2021; 23:168. [PMID: 34127053 PMCID: PMC8201808 DOI: 10.1186/s13075-021-02545-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
Twenty to thirty percent of psoriasis (Pso) patients will develop psoriatic arthritis (PsA). Detection of Pso patients that are (at risk for) developing PsA is essential to prevent structural damage. We conducted a systematic search of five bibliographic databases, up to May 2020. We searched for studies assessing markers (clinical, laboratory, genetic) associated with the development or presence of PsA in Pso patients. Study selection and quality assessment of the included studies was performed, followed by a qualitative best evidence synthesis to determine the level of evidence for a marker and its association with concomitant/developing PsA in Pso. Overall, 259 possible markers were identified in 119 studies that met the inclusion criteria. Laboratory markers related to inflammation and bone metabolism reached a strong level of evidence for the association (not prediction) of PsA in Pso. Only CXCL10 showed strong evidence for a positive predictive value for PsA in Pso. The importance of timely detecting PsA in a Pso population, and finding more (bio)markers contributing to early detection, remains high.
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Affiliation(s)
- Michelle L M Mulder
- Department of Rheumatology, Sint Maartenskliniek, PO box 9011, 6500 GM, Nijmegen, The Netherlands. .,Radboud Institute for Health Sciences (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Tamara W van Hal
- Department of Rheumatology, Sint Maartenskliniek, PO box 9011, 6500 GM, Nijmegen, The Netherlands.,Radboud Institute for Health Sciences (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mark H Wenink
- Department of Rheumatology, Sint Maartenskliniek, PO box 9011, 6500 GM, Nijmegen, The Netherlands
| | - Hans J P M Koenen
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Elke M G J de Jong
- Radboud Institute for Health Sciences (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud University, Nijmegen, The Netherlands.,Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Juul M P A van den Reek
- Radboud Institute for Health Sciences (RIHS), Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Dermatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johanna E Vriezekolk
- Department of Rheumatology, Sint Maartenskliniek, PO box 9011, 6500 GM, Nijmegen, The Netherlands
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23
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Glanville KP, Coleman JRI, O'Reilly PF, Galloway J, Lewis CM. Investigating Pleiotropy Between Depression and Autoimmune Diseases Using the UK Biobank. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 1:48-58. [PMID: 34278373 PMCID: PMC8262258 DOI: 10.1016/j.bpsgos.2021.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/01/2023] Open
Abstract
Background Epidemiological studies report increased comorbidity between depression and autoimmune diseases. The role of shared genetic influences in the observed comorbidity is unclear. We investigated the evidence for pleiotropy between these traits in the UK Biobank (UKB). Methods We defined autoimmune and depression cases using hospital episode statistics, self-reported conditions and medications, and mental health questionnaires. Pairwise comparisons of depression prevalence between autoimmune cases and controls, and vice versa, were performed. Cross-trait polygenic risk score (PRS) analyses tested for pleiotropy, i.e., whether PRSs for depression could predict autoimmune disease status, and vice versa. Results We identified 28,479 cases of autoimmune diseases (pooling across 14 traits) and 324,074 autoimmune controls, and 65,075 cases of depression and 232,552 depression controls. The prevalence of depression was significantly higher in autoimmune cases than in controls, and similarly, the prevalence of autoimmune disease was higher in depression cases than in controls. PRSs for myasthenia gravis and psoriasis were significantly higher in depression cases than in controls (p < 5.2 × 10-5, R 2 ≤ 0.04%). PRSs for depression were significantly higher in inflammatory bowel disease, psoriasis, psoriatic arthritis, rheumatoid arthritis, and type 1 diabetes cases than in controls (p < 5.8 × 10-5, R 2 range = 0.06%-0.27%), and lower in celiac disease cases than in controls (p < 5.4 × 10-7, R 2 range = 0.11%-0.15%). Conclusions Consistent with the literature, depression was more common in individuals with autoimmune diseases than in controls, and vice versa. PRSs showed some evidence for involvement of shared genetic factors, but the modest R 2 values suggest that shared genetic architecture accounts for a small proportion of the increased risk across traits.
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Affiliation(s)
- Kylie P Glanville
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Jonathan R I Coleman
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre, South London and Maudsley NHS Trust, King's College London, London, United Kingdom
| | - Paul F O'Reilly
- Department Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York
| | - James Galloway
- Department of Inflammation Biology, King's College London, London, United Kingdom
| | - Cathryn M Lewis
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre, South London and Maudsley NHS Trust, King's College London, London, United Kingdom.,Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
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24
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O'Rielly DD, Rahman P. Clinical and molecular significance of genetic loci associated with psoriatic arthritis. Best Pract Res Clin Rheumatol 2021; 35:101691. [PMID: 34020887 DOI: 10.1016/j.berh.2021.101691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Psoriatic arthritis (PsA) is caused by a combination of environmental and multiple genetic factors, with clear evidence for a strong genetic basis. The remarkable accumulation of knowledge gained from genetic, pharmacogenetic, and therapeutic response of biologic agents in PsA has fundamentally changed and advanced our understanding of disease pathogenesis and has identified key signalling pathways. However, only one-quarter of the genetic contribution of PsA has been accounted for; and dissecting the genetic contributors of the cutaneous disease from those that would identify joint disease has been challenging. More importantly, the clinical utility of multiple proposed loci is unclear. In this review, we summarize the potential clinical relevance from established genetic associations and provide insight on the proposed molecular pathways that arise from these associations.
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Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Memorial University, Craig L Dobbin Genetics Research Centre, Suite 3M500, 300 Prince Philip Drive, St. John's, NL, A1B3V6, Canada
| | - Proton Rahman
- St. Clare's Mercy Hospital, 154 LeMarchant Rd, St. John's, Newfoundland, A1C5B8, Canada.
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25
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Wu D, Wong P, Lam SHM, Li EK, Qin L, Tam LS, Gu J. The causal effect of interleukin-17 on the risk of psoriatic arthritis: a Mendelian randomization study. Rheumatology (Oxford) 2021; 60:1963-1973. [PMID: 33188428 DOI: 10.1093/rheumatology/keaa629] [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: 03/21/2020] [Revised: 07/24/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To determine causal associations between genetically predicted TNF-α, IL-12p70 and IL-17 levels and risk of PsA. METHODS The publicly available summary-level findings from genome-wide association studies (GWAS) was used to identify loci influencing normal physiological concentrations of TNF-α, IL-12p70 and IL-17 (n = 8293) among healthy individuals as exposure and a GWAS for PsA from the UK Biobank (PsA = 900, control = 462 033) as the outcome. A two-sample Mendelian randomization (MR) analysis was performed using the inverse-variance weighted (IVW), weighted median and MR-Egger regression methods. Sensitivity analysis and MR-Egger regression analysis were performed to evaluate the heterogeneity and pleiotropic effects of each variant. RESULTS Single-nucleotide polymorphisms (SNPs) at genome-wide significance from GWASs on TNF-α, IL-12p70 and IL-17 were identified as the instrumental variables. The IVW method indicated a causal association between increased IL-17 level and risk of PsA (β = -0.00186 per allele, s.e. = 0.00043, P = 0.002). Results were consistent in the weighted median method (β = -0.00145 per allele, s.e. = 0.00059, P = 0.014) although the MR-Egger method suggested a non-significant association (β = -0.00133 per allele, s.e. = 0.00087; P = 0.087). Single SNP MR results revealed that the C allele of rs117556572 was robustly associated with risk of PsA (β = 0.00210, s.e. = 0.00069, P = 0.002). However, no evidence for a causal effect was observed between TNF-α, IL-12p70, decreased IL-17 levels and risk of PsA. CONCLUSION Our findings provide preliminary evidence that genetic variants predisposing to higher physiological IL-17 level are associated with decreased risk of PsA.
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Affiliation(s)
- Dongze Wu
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Priscilla Wong
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Steven H M Lam
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Edmund K Li
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ling Qin
- Bone Quality and Health Centre of the Department of Orthopedics & Traumatology, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Lai-Shan Tam
- Department of Medicine & Therapeutics, The Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Jieruo Gu
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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26
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Insights into the pathogenesis of psoriatic arthritis from genetic studies. Semin Immunopathol 2021; 43:221-234. [PMID: 33712923 DOI: 10.1007/s00281-021-00843-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/19/2021] [Indexed: 12/20/2022]
Abstract
Psoriatic arthritis (PsA) is a relatively common inflammatory arthritis, a spondyloarthritis (SpA), that occurs most often in patients with psoriasis, a common immune-mediated inflammatory skin disease. Both psoriasis and PsA are highly heritable. Genetic and recent genomic studies have identified variants associated with psoriasis and PsA, but variants differentiating psoriasis from PsA are few. In this review, we describe recent developments in understanding the genetic burden of PsA, linkage, association and epigenetic studies. Using pathway analysis, we provide further insights into the similarities and differences between PsA and psoriasis, as well as between PsA and other immune-mediated inflammatory diseases, particularly ankylosing spondylitis, another SpA. Environmental factors that may trigger PsA in patients with psoriasis are also reviewed. To further understand the pathogenetic differences between PsA and psoriasis as well as other SpA, larger cohort studies of well-phenotyped subjects with integrated analysis of genomic, epigenomic, transcriptomic, proteomic and metabolomic data using interomic system biology approaches are required.
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27
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Caputo V, Strafella C, Termine A, Dattola A, Mazzilli S, Lanna C, Cosio T, Campione E, Novelli G, Giardina E, Cascella R. Overview of the molecular determinants contributing to the expression of Psoriasis and Psoriatic Arthritis phenotypes. J Cell Mol Med 2020; 24:13554-13563. [PMID: 33128843 PMCID: PMC7754002 DOI: 10.1111/jcmm.15742] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Psoriasis and psoriatic arthritis are multifactorial chronic disorders whose etiopathogenesis essentially derives from the alteration of several signalling pathways and the co-occurrence of genetic, epigenetic and non-genetic susceptibility factors that altogether affect the functional and structural property of the skin. Although shared and differential susceptibility genes and molecular pathways are known to contribute to the onset of pathological phenotypes, further research is needed to dissect the molecular causes of psoriatic disease and its progression towards Psoriatic Arthritis. This review will therefore be addressed to explore differences and similarities in the etiopathogenesis and progression of both disorders, with a particular focus on genes involved in the maintenance of the skin structure and integrity (keratins and collagens), modulation of patterns of recognition (through Toll-like receptors and dectin-1) and immuno-inflammatory response (by NLRP3-dependent inflammasome) to microbial pathogens. In addition, special emphasis will be given to the contribution of epigenetic elements (methylation pattern, non-coding RNAs, chromatin modifiers and 3D genome organization) to the etiopathogenesis and progression of psoriasis and psoriatic arthritis. The evidence discussed in this review highlights how the knowledge of patients' clinical and (epi)genomic make-up could be helpful for improving the available therapeutic strategies for psoriasis and psoriatic arthritis treatment.
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Affiliation(s)
- Valerio Caputo
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Claudia Strafella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Andrea Termine
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Annunziata Dattola
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Sara Mazzilli
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Caterina Lanna
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Terenzio Cosio
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Elena Campione
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Giuseppe Novelli
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Neuromed Institute IRCCSPozzilliItaly
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
- Department of Biomedicine and PreventionUILDM Lazio Onlus FoundationTor Vergata UniversityRomeItaly
| | - Raffaella Cascella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Department of Biomedical SciencesCatholic University Our Lady of Good CounselTiranaAlbania
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28
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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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29
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Pathogenesis of psoriasis in the "omic" era. Part IV. Epidemiology, genetics, immunopathogenesis, clinical manifestation and treatment of psoriatic arthritis. Postepy Dermatol Alergol 2020; 37:625-634. [PMID: 33239999 PMCID: PMC7675087 DOI: 10.5114/ada.2020.100478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/16/2020] [Indexed: 12/25/2022] Open
Abstract
Psoriatic arthritis (PsA) is a chronic, progressive, inflammatory arthropathy associated with psoriasis as well as a complex pathogenesis. Genetic and environmental factors trigger the development of the immune-mediated auto-inflammatory response in different sites: skin, bone marrow, entheses and synovial tissues. Studies of the last two decades have changed the view of PsA from a mild, non-progressive arthritis to an inflammatory systemic disease with serious health consequences, not only associated with joint dysfunction, but also with an increased risk of cardiovascular disease and socioeconomic consequences with significantly reduced quality of life. The joint damage starts early in the course of the disease, thus early recognition and treatment with modern biological treatments, which may modify the natural history and slow down progression of this debilitating disease, is essential for the patient long-term outcome.
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30
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Two Variants in the NOTCH4 and HLA-C Genes Contribute to Familial Clustering of Psoriasis. Int J Genomics 2020; 2020:6907378. [PMID: 33134369 PMCID: PMC7593743 DOI: 10.1155/2020/6907378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/05/2022] Open
Abstract
Psoriasis is a multifactorial immune-mediated skin disease with a strong genetic background. Previous studies reported that psoriasis with a family history (PFH) and sporadic psoriasis (SP) have a distinct manifestation and genetic predisposition. However, the genetic heterogeneity of PFH and SP in the major histocompatibility complex (MHC) region has not been fully elucidated. To explore genetic variants in the MHC region that drive family aggregation of psoriasis, we included a total of 8,127 psoriasis cases and 9,906 healthy controls from Han Chinese and divided psoriasis into two subtypes, PFH (n = 1,538) and SP (n = 5,262). Then, we calculated the heritability of PFH and SP and performed a large-scale stratified association analysis. We confirmed that variants in the MHC region collectively explained a higher heritability of PFH (16.8%) than SP (13.3%). Further stratified association analysis illustrated that HLA-C∗06:02 and NOTCH4:G511S contribute to the family aggregation of psoriasis, and BTNL2:R281K specifically confers risk for SP. HLA-C∗06:02 and NOTCH4:G511S could partially explain why patients with PFH have a stronger genetic predisposition, more complex phenotypes, and more frequent other autoimmune diseases. The identification of the SP-specific variant BTNL2:R281K revealed that the genetic architecture of SP is not just a subset of PFH.
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31
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McGuirl MR, Smith SP, Sandstede B, Ramachandran S. Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics. Genetics 2020; 215:511-529. [PMID: 32245788 PMCID: PMC7268989 DOI: 10.1534/genetics.120.303096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
Emerging large-scale biobanks pairing genotype data with phenotype data present new opportunities to prioritize shared genetic associations across multiple phenotypes for molecular validation. Past research, by our group and others, has shown gene-level tests of association produce biologically interpretable characterization of the genetic architecture of a given phenotype. Here, we present a new method, Ward clustering to identify Internal Node branch length outliers using Gene Scores (WINGS), for identifying shared genetic architecture among multiple phenotypes. The objective of WINGS is to identify groups of phenotypes, or "clusters," sharing a core set of genes enriched for mutations in cases. We validate WINGS using extensive simulation studies and then combine gene-level association tests with WINGS to identify shared genetic architecture among 81 case-control and seven quantitative phenotypes in 349,468 European-ancestry individuals from the UK Biobank. We identify eight prioritized phenotype clusters and recover multiple published gene-level associations within prioritized clusters.
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Affiliation(s)
- Melissa R McGuirl
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Björn Sandstede
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912
- Data Science Initiative, Brown University, Providence, Rhode Island 02912
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
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32
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Chandran V, Rahman P. Predicting therapeutic response through biomarker analysis in psoriatic arthritis, an example of precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1724509] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Vinod Chandran
- Faculty of Medicine, University of Toronto, Toronto, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Proton Rahman
- Division of Rheumatology, Department of Medicine, Memorial University, St. John’s, Newfoundland, Canada
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33
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Abstract
PURPOSE OF REVIEW The therapeutic response to biologic agents in psoriasis is significantly higher than observed in psoriatic arthritis (PsA). In this review, specific actions to improve treatment outcomes in PsA are discussed. RECENT FINDINGS Increased understanding of disease pathogenesis derived from improved preclinical models and advances in cell-based and molecular technologies provide new tools to identify therapeutic targets. In addition to the important contributions of metabolic comorbidities, chronic pain and the lack of a diagnostic biomarker signal the need for new strategies to improve outcomes. Potential strategies include the following: (1) discover a novel pathway or cellular subset, (2) apply stratification biomarkers to individualize therapy, (3) preclinical intervention, (4) combination therapy, (5) lifestyle modification, (6) address chronic pain and fatigue, and (7) multidisciplinary care. The future holds great promise for enhanced treatment responses in PsA based on improved understanding of individual variation in disease pathophysiology coupled with comprehensive and integrated treatment programs.
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Affiliation(s)
- Christopher Ritchlin
- Allergy, Immunology and Rheumatology Division, Center for Musculoskeletal Research, University of Rochester Medical Center, Box 695, Rochester, NY, 14642, USA.
| | - Jose U Scher
- Department of Medicine, Division of Rheumatology and Psoriatic Arthritis Center, New York University School of Medicine, New York, NY, USA
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34
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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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35
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Preventing psoriatic arthritis: focusing on patients with psoriasis at increased risk of transition. Nat Rev Rheumatol 2019; 15:153-166. [DOI: 10.1038/s41584-019-0175-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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GAG metabolism associated with PsA risk. Nat Rev Rheumatol 2019; 15:64. [DOI: 10.1038/s41584-019-0161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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