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Bianchi M, Kozyrev SV, Notarnicola A, Hultin Rosenberg L, Karlsson Å, Pucholt P, Rothwell S, Alexsson A, Sandling JK, Andersson H, Cooper RG, Padyukov L, Tjärnlund A, Dastmalchi M, Meadows JRS, Pyndt Diederichsen L, Molberg Ø, Chinoy H, Lamb JA, Rönnblom L, Lindblad-Toh K, Lundberg IE. Contribution of Rare Genetic Variation to Disease Susceptibility in a Large Scandinavian Myositis Cohort. Arthritis Rheumatol 2022; 74:342-352. [PMID: 34279065 DOI: 10.1002/art.41929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of complex autoimmune conditions characterized by inflammation in skeletal muscle and extramuscular compartments, and interferon (IFN) system activation. We undertook this study to examine the contribution of genetic variation to disease susceptibility and to identify novel avenues for research in IIMs. METHODS Targeted DNA sequencing was used to mine coding and potentially regulatory single nucleotide variants from ~1,900 immune-related genes in a Scandinavian case-control cohort of 454 IIM patients and 1,024 healthy controls. Gene-based aggregate testing, together with rare variant- and gene-level enrichment analyses, was implemented to explore genotype-phenotype relations. RESULTS Gene-based aggregate tests of all variants, including rare variants, identified IFI35 as a potential genetic risk locus for IIMs, suggesting a genetic signature of type I IFN pathway activation. Functional annotation of the IFI35 locus highlighted a regulatory network linked to the skeletal muscle-specific gene PTGES3L, as a potential candidate for IIM pathogenesis. Aggregate genetic associations with AGER and PSMB8 in the major histocompatibility complex locus were detected in the antisynthetase syndrome subgroup, which also showed a less marked genetic signature of the type I IFN pathway. Enrichment analyses indicated a burden of synonymous and noncoding rare variants in IIM patients, suggesting increased disease predisposition associated with these classes of rare variants. CONCLUSION Our study suggests the contribution of rare genetic variation to disease susceptibility in IIM and specific patient subgroups, and pinpoints genetic associations consistent with previous findings by gene expression profiling. These features highlight genetic profiles that are potentially relevant to disease pathogenesis.
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Affiliation(s)
- Matteo Bianchi
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | - Sergey V Kozyrev
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | | | | | - Åsa Karlsson
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | | | | | | | | | | | - Robert G Cooper
- Aintree University Hospital, MRC-Arthritis Research UK Centre for integrated Research into Musculoskeletal Ageing, and University of Liverpool, Liverpool, UK
| | - Leonid Padyukov
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anna Tjärnlund
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Maryam Dastmalchi
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | - Øyvind Molberg
- Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hector Chinoy
- National Institute for Health Research Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, University of Manchester, and Manchester Academic Health Science Centre, Manchester, UK, and Salford Royal NHS Foundation Trust, Salford, UK
| | | | | | - Kerstin Lindblad-Toh
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden, and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ingrid E Lundberg
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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2
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Norheim KB, Imgenberg-Kreuz J, Alexsson A, Johnsen SJA, Bårdsen K, Brun JG, Dehkordi RK, Theander E, Mandl T, Jonsson R, Ng WF, Lessard CJ, Rasmussen A, Sivilis K, Ronnblom L, Omdal R. Genetic variants at the RTP4/MASP1 locus are associated with fatigue in Scandinavian patients with primary Sjögren's syndrome. RMD Open 2021; 7:rmdopen-2021-001832. [PMID: 34907023 PMCID: PMC8671987 DOI: 10.1136/rmdopen-2021-001832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/19/2021] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVES Fatigue is common and severe in primary Sjögren's syndrome (pSS). The aim of this study was to identify genetic determinants of fatigue in pSS through a genome-wide association study. METHODS Patients with pSS from Norway, Sweden, UK and USA with fatigue and genotype data available were included. After genotype imputation and quality control, 682 patients and 4 966 157 genetic markers were available. Association analysis in each cohort using linear regression with fatigue as a continuous variable and meta-analyses between the cohorts were performed. RESULTS Meta-analysis of the Norwegian and Swedish cohorts identified five polymorphisms within the same linkage disequilibrium block at the receptor transporter protein 4 (RTP4)/MASP1 locus associated with fatigue with genome-wide significance (GWS) (p<5×10-8). Patients homozygous for the major allele scored 25 mm higher on the fatigue Visual Analogue Scale than patients homozygous for the minor allele. There were no variants associated with fatigue with GWS in meta-analyses of the US/UK cohorts, or all four cohorts. RTP4 expression in pSS B cells was upregulated and positively correlated with the type I interferon score. Expression quantitative trait loci effects in whole blood for fatigue-associated variants at RTP4/MASP1 and levels of RTP4 and MASP1 expression were identified. CONCLUSION Genetic variations at RTP4/MASP1 are associated with fatigue in Scandinavian pSS patients. RTP4 encodes a Golgi chaperone that influences opioid pain receptor function and MASP1 is involved in complement activation. These results add evidence for genetic influence over fatigue in pSS.
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Affiliation(s)
- Katrine Brække Norheim
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Juliana Imgenberg-Kreuz
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway,Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Svein Joar Auglænd Johnsen
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Bårdsen
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Johan Gorgas Brun
- Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Rezvan Kiani Dehkordi
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Elke Theander
- Department of Clinical Science, Lund University, Lund, Sweden
| | - Thomas Mandl
- Department of Clinical Science, Lund University, Lund, Sweden
| | - Roland Jonsson
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Wan-Fai Ng
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK,Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher J Lessard
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy Sivilis
- Translational Sciences, Rheumatology, Janssen Pharmaceutical Companies of Johnson and Johnson, New York, New York, USA
| | - Lars Ronnblom
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway,Department of Clinical Science, University of Bergen, Bergen, Norway
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3
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Bolin K, Imgenberg-Kreuz J, Leonard D, Sandling JK, Alexsson A, Pucholt P, Haarhaus ML, Almlöf JC, Nititham J, Jönsen A, Sjöwall C, Bengtsson AA, Rantapää-Dahlqvist S, Svenungsson E, Gunnarsson I, Syvänen AC, Lerang K, Troldborg A, Voss A, Molberg Ø, Jacobsen S, Criswell L, Rönnblom L, Nordmark G. Variants in BANK1 are associated with lupus nephritis of European ancestry. Genes Immun 2021; 22:194-202. [PMID: 34127828 PMCID: PMC8277572 DOI: 10.1038/s41435-021-00142-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022]
Abstract
The genetic background of lupus nephritis (LN) has not been completely elucidated. We performed a case-only study of 2886 SLE patients, including 947 (33%) with LN. Renal biopsies were available from 396 patients. The discovery cohort (Sweden, n = 1091) and replication cohort 1 (US, n = 962) were genotyped on the Immunochip and replication cohort 2 (Denmark/Norway, n = 833) on a custom array. Patients with LN, proliferative nephritis, or LN with end-stage renal disease were compared with SLE without nephritis. Six loci were associated with LN (p < 1 × 10−4, NFKBIA, CACNA1S, ITGA1, BANK1, OR2Y, and ACER3) in the discovery cohort. Variants in BANK1 showed the strongest association with LN in replication cohort 1 (p = 9.5 × 10−4) and proliferative nephritis in a meta-analysis of discovery and replication cohort 1. There was a weak association between BANK1 and LN in replication cohort 2 (p = 0.052), and in the meta-analysis of all three cohorts the association was strengthened (p = 2.2 × 10−7). DNA methylation data in 180 LN patients demonstrated methylation quantitative trait loci (meQTL) effects between a CpG site and BANK1 variants. To conclude, we describe genetic variations in BANK1 associated with LN and evidence for genetic regulation of DNA methylation within the BANK1 locus. This indicates a role for BANK1 in LN pathogenesis.
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Affiliation(s)
- Karin Bolin
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juliana Imgenberg-Kreuz
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Malena Loberg Haarhaus
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Stockholm, Stockholm, Sweden
| | - Jonas Carlsson Almlöf
- Molecular Medicine, Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andreas Jönsen
- Department of Rheumatology, Lund University, Lund, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | | | - Elisabet Svenungsson
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Stockholm, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Stockholm, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Molecular Medicine, Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karoline Lerang
- Department of Rheumatology, University of Oslo, Oslo, Norway
| | - Anne Troldborg
- Department of Rheumatology, Aarhus University Hospital and Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Øyvind Molberg
- Department of Rheumatology, University of Oslo, Oslo, Norway
| | - Søren Jacobsen
- Department of Clinical Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lindsey Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lars Rönnblom
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Abdulla M, Alexsson A, Sundström C, Ladenvall C, Mansouri L, Lindskog C, Berglund M, Cavelier L, Enblad G, Hollander P, Amini RM. PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS. Acta Oncol 2021; 60:531-538. [PMID: 33579170 DOI: 10.1080/0284186x.2021.1881161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Programmed cell death 1 (PD-1) and its ligands PD-L1 and PD-L2, as well as Indoleamine 2,3-deoxygenase (IDO1) can be expressed both by tumor and microenvironmental cells and are crucial for tumor immune escape. We aimed to evaluate the role of PD-1, its ligands and IDO1 in a cohort of patients with primary diffuse large B-cell lymphoma of the CNS (PCNSL). MATERIAL AND METHODS Tissue microarrays (TMAs) were constructed in 45 PCNSL cases. RNA extraction from whole tissue sections and RNA sequencing were successfully performed in 33 cases. Immunohistochemical stainings for PD-1, PD-L1/paired box protein 5 (PAX-5), PD-L2/PAX-5 and IDO1, and Epstein-Barr virus encoding RNA (EBER) in situ hybridization were analyzed. RESULTS High proportions of PD-L1 and PD-L2 positive tumor cells were observed in 11% and 9% of cases, respectively. High proportions of PD-L1 and PD-L2 positive leukocytes were observed in 55% and 51% of cases, respectively. RNA sequencing revealed that gene expression of IDO1 was high in patients with high proportion of PD-L1 positive leukocytes (p = .01). Protein expression of IDO1 in leukocytes was detected in 14/45 cases, in 79% of these cases a high proportion of PD-L1 positive leukocytes was observed. Gene expression of IDO1 was high in EBER-positive cases (p = .0009) and protein expression of IDO1 was detected in five of six EBER-positive cases. CONCLUSION Our study shows a significant association between gene and protein expression of IDO1 and protein expression of PD-L1 in the tumor microenvironment of PCNSL, possibly of importance for prediction of response to immunotherapies.
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Affiliation(s)
- Maysaa Abdulla
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University and University Hospital, Uppsala, Sweden
| | - Andrei Alexsson
- Clinical Genomics Uppsala, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christer Sundström
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University and University Hospital, Uppsala, Sweden
| | - Claes Ladenvall
- Clinical Genomics Uppsala, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mattias Berglund
- Experimental and Clinical Oncology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Clinical Genomics Uppsala, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunilla Enblad
- Experimental and Clinical Oncology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter Hollander
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University and University Hospital, Uppsala, Sweden
| | - Rose-Marie Amini
- Clinical and Experimental Pathology, Department of Immunology, Genetics and Pathology, Uppsala University and University Hospital, Uppsala, Sweden
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5
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Reid S, Hagberg N, Sandling JK, Alexsson A, Pucholt P, Sjöwall C, Lerang K, Jönsen A, Gunnarsson I, Syvänen AC, Troldborg AM, Voss A, Bengtsson AA, Molberg Ø, Jacobsen S, Svenungsson E, Rönnblom L, Leonard D. Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus. Ann Rheum Dis 2021; 80:1183-1189. [PMID: 33766895 PMCID: PMC8372395 DOI: 10.1136/annrheumdis-2020-219727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 03/06/2021] [Indexed: 12/17/2022]
Abstract
Objective To investigate how genetics influence the risk of smoking-related systemic lupus erythematosus (SLE) manifestations. Methods Patients with SLE (ndiscovery cohort=776, nreplication cohort=836) were genotyped using the 200K Immunochip single nucleotide polymorphisms (SNP) Array (Illumina) and a custom array. Sixty SNPs with SLE association (p<5.0×10−8) were analysed. Signal transducer and activator of transcription 4 (STAT4) activation was assessed in in vitro stimulated peripheral blood mononuclear cells from healthy controls (n=45). Results In the discovery cohort, smoking was associated with myocardial infarction (MI) (OR 1.96 (95% CI 1.09 to 3.55)), with a greater effect in patients carrying any rs11889341 STAT4 risk allele (OR 2.72 (95% CI 1.24 to 6.00)) or two risk alleles (OR 8.27 (95% CI 1.48 to 46.27)). Smokers carrying the risk allele also displayed an increased risk of nephritis (OR 1.47 (95% CI 1.06 to 2.03)). In the replication cohort, the high risk of MI in smokers carrying the risk allele and the association between the STAT4 risk allele and nephritis in smokers were confirmed (OR 6.19 (95% CI 1.29 to 29.79) and 1.84 (95% CI 1.05 to 3.29), respectively). The interaction between smoking and the STAT4 risk allele resulted in further increase in the risk of MI (OR 2.14 (95% CI 1.01 to 4.62)) and nephritis (OR 1.53 (95% CI 1.08 to 2.17)), with 54% (MI) and 34% (nephritis) of the risk attributable to the interaction. Levels of interleukin-12-induced phosphorylation of STAT4 in CD8+ T cells were higher in smokers than in non-smokers (mean geometric fluorescence intensity 1063 vs 565, p=0.0063). Lastly, the IL12A rs564799 risk allele displayed association with MI in both cohorts (OR 1.53 (95% CI 1.01 to 2.31) and 2.15 (95% CI 1.08 to 4.26), respectively). Conclusions Smoking in the presence of the STAT4 risk gene variant appears to increase the risk of MI and nephritis in SLE. Our results also highlight the role of the IL12−STAT4 pathway in SLE-cardiovascular morbidity.
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Affiliation(s)
- Sarah Reid
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niklas Hagberg
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linkoping, Sweden
| | - Karoline Lerang
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Andreas Jönsen
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne Margrethe Troldborg
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Anders A Bengtsson
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Øyvind Molberg
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Søren Jacobsen
- Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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6
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Sandling JK, Pucholt P, Hultin Rosenberg L, Farias FHG, Kozyrev SV, Eloranta ML, Alexsson A, Bianchi M, Padyukov L, Bengtsson C, Jonsson R, Omdal R, Lie BA, Massarenti L, Steffensen R, Jakobsen MA, Lillevang ST, Lerang K, Molberg Ø, Voss A, Troldborg A, Jacobsen S, Syvänen AC, Jönsen A, Gunnarsson I, Svenungsson E, Rantapää-Dahlqvist S, Bengtsson AA, Sjöwall C, Leonard D, Lindblad-Toh K, Rönnblom L. Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing. Ann Rheum Dis 2020; 80:109-117. [PMID: 33037003 PMCID: PMC7788061 DOI: 10.1136/annrheumdis-2020-218636] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/02/2023]
Abstract
Objectives Systemic lupus erythematosus (SLE) is an autoimmune disease with extensive heterogeneity in disease presentation between patients, which is likely due to an underlying molecular diversity. Here, we aimed at elucidating the genetic aetiology of SLE from the immunity pathway level to the single variant level, and stratify patients with SLE into distinguishable molecular subgroups, which could inform treatment choices in SLE. Methods We undertook a pathway-centred approach, using sequencing of immunological pathway genes. Altogether 1832 candidate genes were analysed in 958 Swedish patients with SLE and 1026 healthy individuals. Aggregate and single variant association testing was performed, and we generated pathway polygenic risk scores (PRS). Results We identified two main independent pathways involved in SLE susceptibility: T lymphocyte differentiation and innate immunity, characterised by HLA and interferon, respectively. Pathway PRS defined pathways in individual patients, who on average were positive for seven pathways. We found that SLE organ damage was more pronounced in patients positive for the T or B cell receptor signalling pathways. Further, pathway PRS-based clustering allowed stratification of patients into four groups with different risk score profiles. Studying sets of genes with priors for involvement in SLE, we observed an aggregate common variant contribution to SLE at genes previously reported for monogenic SLE as well as at interferonopathy genes. Conclusions Our results show that pathway risk scores have the potential to stratify patients with SLE beyond clinical manifestations into molecular subsets, which may have implications for clinical follow-up and therapy selection.
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Affiliation(s)
- Johanna K Sandling
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lina Hultin Rosenberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fabiana H G Farias
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Psychiatry, Washington University, St. Louis, Missouri, USA
| | - Sergey V Kozyrev
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Christine Bengtsson
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roald Omdal
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Clinical Immunology unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo, Oslo, Norway
| | - Laura Massarenti
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University, Aalborg, Denmark
| | - Marianne A Jakobsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Søren T Lillevang
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | | | - Karoline Lerang
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Øyvind Molberg
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Anne Troldborg
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.,Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Jacobsen
- Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | - Anders A Bengtsson
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
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Reid S, Alexsson A, Frodlund M, Morris D, Sandling JK, Bolin K, Svenungsson E, Jönsen A, Bengtsson C, Gunnarsson I, Illescas Rodriguez V, Bengtsson A, Arve S, Rantapää-Dahlqvist S, Eloranta ML, Syvänen AC, Sjöwall C, Vyse TJ, Rönnblom L, Leonard D. High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus. Ann Rheum Dis 2019; 79:363-369. [PMID: 31826855 PMCID: PMC7034364 DOI: 10.1136/annrheumdis-2019-216227] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 12/23/2022]
Abstract
Objectives To investigate associations between a high genetic disease risk and disease severity in patients with systemic lupus erythematosus (SLE). Methods Patients with SLE (n=1001, discovery cohort and n=5524, replication cohort) and healthy controls (n=2802 and n=9859) were genotyped using a 200K Immunochip single nucleotide polymorphism array. A genetic risk score (GRS) was assigned to each individual based on 57 SLE risk loci. Results SLE was more prevalent in the high, compared with the low, GRS-quartile (OR 12.32 (9.53 to 15.71), p=7.9×10–86 and OR 7.48 (6.73 to 8.32), p=2.2×10–304 for the discovery and the replication cohorts, respectively). In the discovery cohort, patients in the high GRS-quartile had a 6-year earlier mean disease onset (HR 1.47 (1.22 to 1.75), p=4.3×10–5), displayed higher prevalence of damage accrual (OR 1.47 (1.06 to 2.04), p=2.0×10–2), renal disorder (OR 2.22 (1.50 to 3.27), p=5.9×10–5), anti-dsDNA (OR 1.83 (1.19 to 2.81), p=6.1×10–3), end-stage renal disease (ESRD) (OR 5.58 (1.50 to 20.79), p=1.0×10–2), proliferative nephritis (OR 2.42 (1.30 to 4.49), p=5.1×10–3), anti-cardiolipin-IgG (OR 1.89 (1.13 to 3.18), p=1.6×10–2), anti-β2-glycoprotein-I-IgG (OR 2.29 (1.29 to 4.06), p=4.8×10–3) and positive lupus anticoagulant test (OR 2.12 (1.16 to 3.89), p=1.5×10–2) compared with patients in the low GRS-quartile. Survival analysis showed earlier onset of the first organ damage (HR 1.51 (1.04 to 2.25), p=3.7×10–2), first cardiovascular event (HR 1.65 (1.03 to 2.64), p=2.6×10–2), nephritis (HR 2.53 (1.72 to 3.71), p=9.6×10–7), ESRD (HR 6.78 (1.78 to 26.86), p=6.5×10–3) and decreased overall survival (HR 1.83 (1.02 to 3.30), p=4.3×10–2) in high to low quartile comparison. Conclusions A high GRS is associated with increased risk of organ damage, renal dysfunction and all-cause mortality. Our results indicate that genetic profiling may be useful for predicting outcomes in patients with SLE.
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Affiliation(s)
- Sarah Reid
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Martina Frodlund
- Rheumatology/Division of Neuro and Inflammation Sciences, Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
| | - David Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Johanna K Sandling
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Karin Bolin
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Elisabet Svenungsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Jönsen
- Rheumatology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Christine Bengtsson
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Iva Gunnarsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vera Illescas Rodriguez
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Bengtsson
- Rheumatology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Sabine Arve
- Rheumatology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Maija-Leena Eloranta
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christopher Sjöwall
- Rheumatology/Division of Neuro and Inflammation Sciences, Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
| | - Timothy James Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Lars Rönnblom
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Odqvist L, Jevnikar Z, Riise R, Öberg L, Rhedin M, Leonard D, Yrlid L, Jackson S, Mattsson J, Nanda S, Cohen P, Knebel A, Arthur S, Thörn K, Svenungsson E, Jönsen A, Gunnarsson I, Tandre K, Alexsson A, Kastbom A, Rantapää-Dahlqvist S, Eloranta ML, Syvänen AC, Bengtsson A, Johansson P, Sandling JK, Sjöwall C, Rönnblom L, Collins B, Vaarala O. Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus. Ann Rheum Dis 2019; 78:1363-1370. [PMID: 31300459 PMCID: PMC6788882 DOI: 10.1136/annrheumdis-2019-215434] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/05/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of systemic lupus erythematosus (SLE) and rheumatoid arthritis. A20 is a negative regulator of NF-κB but the role of its DUB domain and related genetic variants remain unclear. We aimed to study the functional effects of A20 DUB-domain alterations in immune cells and understand its link to SLE pathogenesis. METHODS CRISPR/Cas9 was used to generate human U937 monocytes with A20 DUB-inactivating C103A knock-in (KI) mutation. Whole genome RNA-sequencing was used to identify differentially expressed genes between WT and C103A KI cells. Functional studies were performed in A20 C103A U937 cells and in immune cells from A20 C103A mice and genotyped healthy individuals with A20 DUB polymorphism rs2230926. Neutrophil extracellular trap (NET) formation was addressed ex vivo in neutrophils from A20 C103A mice and SLE-patients with rs2230926. RESULTS Genetic disruption of A20 DUB domain in human and murine myeloid cells did not give rise to enhanced NF-κB signalling. Instead, cells with C103A mutation or rs2230926 polymorphism presented an upregulated expression of PADI4, an enzyme regulating protein citrullination and NET formation, two key mechanisms in autoimmune pathology. A20 C103A cells exhibited enhanced protein citrullination and extracellular trap formation, which could be suppressed by selective PAD4 inhibition. Moreover, SLE-patients with rs2230926 showed increased NETs and increased frequency of autoantibodies to citrullinated epitopes. CONCLUSIONS We propose that genetic alterations disrupting the A20 DUB domain mediate increased susceptibility to SLE through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation.
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Affiliation(s)
- Lina Odqvist
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Zala Jevnikar
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Rebecca Riise
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Lisa Öberg
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Magdalena Rhedin
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Linda Yrlid
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Sonya Jackson
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Johan Mattsson
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Sambit Nanda
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Simon Arthur
- Division of Immunology and Cell Signaling, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kristofer Thörn
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Elisabet Svenungsson
- Department of Medicine, Rheumatology Unit, Karolinska Institute, Stockholm, Sweden
| | - Andreas Jönsen
- Skåne University Hospital, Department of Clinical Science Lund, Rheumatology, Lund University, Lund, Sweden
| | - Iva Gunnarsson
- Department of Medicine, Rheumatology Unit, Karolinska Institute, Stockholm, Sweden
| | - Karolina Tandre
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Alf Kastbom
- Department of Rheumatology and Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
| | - Solbritt Rantapää-Dahlqvist
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå Universitet Medicinska fakulteten, Umea, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Anders Bengtsson
- Skåne University Hospital, Department of Clinical Science Lund, Rheumatology, Lund University, Lund, Sweden
| | - Patrik Johansson
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Christopher Sjöwall
- Department of Rheumatology and Department of Clinical and Experimental Medicine, Linköping University, Linkoping, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Barry Collins
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
| | - Outi Vaarala
- Research and Early Development, Respiratory, Inflammation and Autoimmune, BioPharmaceuticals R&D, AstraZeneca R&D Gothenburg, Mölndal, Sweden
- Respiratory, Inflammation and Autoimmunity Department, MedImmune LLC, Gaithersburg, Maryland, USA
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9
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Leonard D, Svenungsson E, Dahlqvist J, Alexsson A, Ärlestig L, Taylor KE, Sandling JK, Bengtsson C, Frodlund M, Jönsen A, Eketjäll S, Jensen-Urstad K, Gunnarsson I, Sjöwall C, Bengtsson AA, Eloranta ML, Syvänen AC, Rantapää-Dahlqvist S, Criswell LA, Rönnblom L. Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis. Ann Rheum Dis 2018. [PMID: 29514802 PMCID: PMC6029634 DOI: 10.1136/annrheumdis-2017-212614] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Objectives Patients with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) have increased risk of cardiovascular disease (CVD). We investigated whether single nucleotide polymorphisms (SNPs) at autoimmunity risk loci were associated with CVD in SLE and RA. Methods Patients with SLE (n=1045) were genotyped using the 200K Immunochip SNP array (Illumina). The allele frequency was compared between patients with and without different manifestations of CVD. Results were replicated in a second SLE cohort (n=1043) and in an RA cohort (n=824). We analysed publicly available genetic data from general population, performed electrophoretic mobility shift assays and measured cytokine levels and occurrence of antiphospholipid antibodies (aPLs). Results We identified two new putative risk loci associated with increased risk for CVD in two SLE populations, which remained after adjustment for traditional CVD risk factors. An IL19 risk allele, rs17581834(T) was associated with stroke/myocardial infarction (MI) in SLE (OR 2.3 (1.5 to 3.4), P=8.5×10−5) and RA (OR 2.8 (1.4 to 5.6), P=3.8×10−3), meta-analysis (OR 2.5 (2.0 to 2.9), P=3.5×10−7), but not in population controls. The IL19 risk allele affected protein binding, and SLE patients with the risk allele had increased levels of plasma-IL10 (P=0.004) and aPL (P=0.01). An SRP54-AS1 risk allele, rs799454(G) was associated with stroke/transient ischaemic attack in SLE (OR 1.7 (1.3 to 2.2), P=2.5×10−5) but not in RA. The SRP54-AS1 risk allele is an expression quantitative trait locus for four genes. Conclusions The IL19 risk allele was associated with stroke/MI in SLE and RA, but not in the general population, indicating that shared immune pathways may be involved in the CVD pathogenesis in inflammatory rheumatic diseases.
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Affiliation(s)
- Dag Leonard
- Department of Medical Sciences, Science for Life Laboratory, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Elisabet Svenungsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Dahlqvist
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Science for Life Laboratory, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lisbeth Ärlestig
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Kimberly E Taylor
- University of California, San Francisco, Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, San Francisco, California, USA
| | - Johanna K Sandling
- Department of Medical Sciences, Science for Life Laboratory, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Christine Bengtsson
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Martina Frodlund
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Andreas Jönsen
- Department of Rheumatology, Skåne University Hospital, Lund, Sweden
| | - Susanna Eketjäll
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Integrated Cardio Metabolic Centre, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Jensen-Urstad
- Department of Clinical Physiology, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine, Rheumatology Unit, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sjöwall
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | | | - Maija-Leena Eloranta
- Department of Medical Sciences, Science for Life Laboratory, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Science for Life Laboratory, Molecular Medicine, Uppsala University, Uppsala, Sweden
| | | | - Lindsey A Criswell
- University of California, San Francisco, Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, San Francisco, California, USA
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Rheumatology, Uppsala University, Uppsala, Sweden
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10
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Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, Alexsson A, Nordmark G, Eloranta ML, Rantapää-Dahlqvist S, Bengtsson AA, Jönsen A, Padyukov L, Gunnarsson I, Svenungsson E, Sjöwall C, Rönnblom L, Syvänen AC, Sandling JK. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann Rheum Dis 2018; 77:736-743. [PMID: 29437559 PMCID: PMC5909746 DOI: 10.1136/annrheumdis-2017-212379] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 11/18/2022]
Abstract
Objectives Systemic lupus erythematosus (SLE) is a chronic autoimmune condition with heterogeneous presentation and complex aetiology where DNA methylation changes are emerging as a contributing factor. In order to discover novel epigenetic associations and investigate their relationship to genetic risk for SLE, we analysed DNA methylation profiles in a large collection of patients with SLE and healthy individuals. Methods DNA extracted from blood from 548 patients with SLE and 587 healthy controls were analysed on the Illumina HumanMethylation 450 k BeadChip, which targets 485 000 CpG sites across the genome. Single nucleotide polymorphism (SNP) genotype data for 196 524 SNPs on the Illumina ImmunoChip from the same individuals were utilised for methylation quantitative trait loci (cis-meQTLs) analyses. Results We identified and replicated differentially methylated CpGs (DMCs) in SLE at 7245 CpG sites in the genome. The largest methylation differences were observed at type I interferon-regulated genes which exhibited decreased methylation in SLE. We mapped cis-meQTLs and identified genetic regulation of methylation levels at 466 of the DMCs in SLE. The meQTLs for DMCs in SLE were enriched for genetic association to SLE, and included seven SLE genome-wide association study (GWAS) loci: PTPRC (CD45), MHC-class III, UHRF1BP1, IRF5, IRF7, IKZF3 and UBE2L3. In addition, we observed association between genotype and variance of methylation at 20 DMCs in SLE, including at the HLA-DQB2 locus. Conclusions Our results suggest that several of the genetic risk variants for SLE may exert their influence on the phenotype through alteration of DNA methylation levels at regulatory regions of target genes.
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Affiliation(s)
- Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Andrei Alexsson
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Gunnel Nordmark
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Maija-Leena Eloranta
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | | | - Anders A Bengtsson
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sjöwall
- Department of Clinical and Experimental Medicine, Rheumatology/Division of Neuro and Inflammation Sciences, Linköping University, Linköping, Sweden
| | - Lars Rönnblom
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
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11
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Berggren O, Hagberg N, Alexsson A, Weber G, Rönnblom L, Eloranta ML. Plasmacytoid dendritic cells and RNA-containing immune complexes drive expansion of peripheral B cell subsets with an SLE-like phenotype. PLoS One 2017; 12:e0183946. [PMID: 28846748 PMCID: PMC5573130 DOI: 10.1371/journal.pone.0183946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/15/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Hyperactive B cells and a continuous interferon (IFN)-α production by plasmacytoid dendritic cells (pDCs) play a key role in systemic lupus erythematosus (SLE). We asked whether the interaction between B cells and pDCs stimulated with RNA-containing immune complexes affects peripheral B cell subsets. METHODS B cells and pDCs were isolated from blood of healthy individuals and stimulated with immune complexes consisting of SLE-IgG and U1snRNP (RNA-IC). Expression of cell surface molecules as well as IL-6 and IL-10 production were determined by flow cytometry and immunoassays. Gene expression profiles were determined by a NanoString nCounter expression array. RESULTS We found a remarkable increase of double negative CD27-IgD- B cells, from 7% within fresh CD19+ B cells to 37% in the RNA-IC-stimulated co-cultures of B cells and pDCs, comparable to the frequency of double negative B cells in SLE patients. Gene expression analysis of the double negative CD27-IgD- and the CD27+IgD- memory B cells revealed that twenty-one genes were differentially expressed between the two B cell subsets (≥ 2-fold, p<0.001). The, IL21R, IL4R, CCL4, CCL3, CD83 and the IKAROS Family Zinc Finger 2 (IKZ2) showed higher expression in the double negative CD27-IgD- B cells. CONCLUSION The interactions between B cells and pDCs together with RNA-containing IC led to an expansion of B cells with similar phenotype as seen in SLE, suggesting that the pDC-B cell crosstalk contributes to the autoimmune feed-forward loop in SLE.
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Affiliation(s)
- Olof Berggren
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niklas Hagberg
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gert Weber
- Department of Molecular Structural Biology, Institute of Biochemistry, Ernst-Moritz-Arndt University of Greifswald, Greifswald, Germany
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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12
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Almlöf JC, Alexsson A, Imgenberg-Kreuz J, Sylwan L, Bäcklin C, Leonard D, Nordmark G, Tandre K, Eloranta ML, Padyukov L, Bengtsson C, Jönsen A, Dahlqvist SR, Sjöwall C, Bengtsson AA, Gunnarsson I, Svenungsson E, Rönnblom L, Sandling JK, Syvänen AC. Novel risk genes for systemic lupus erythematosus predicted by random forest classification. Sci Rep 2017; 7:6236. [PMID: 28740209 PMCID: PMC5524838 DOI: 10.1038/s41598-017-06516-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/13/2017] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies have identified risk loci for SLE, but a large proportion of the genetic contribution to SLE still remains unexplained. To detect novel risk genes, and to predict an individual's SLE risk we designed a random forest classifier using SNP genotype data generated on the "Immunochip" from 1,160 patients with SLE and 2,711 controls. Using gene importance scores defined by the random forest classifier, we identified 15 potential novel risk genes for SLE. Of them 12 are associated with other autoimmune diseases than SLE, whereas three genes (ZNF804A, CDK1, and MANF) have not previously been associated with autoimmunity. Random forest classification also allowed prediction of patients at risk for lupus nephritis with an area under the curve of 0.94. By allele-specific gene expression analysis we detected cis-regulatory SNPs that affect the expression levels of six of the top 40 genes designed by the random forest analysis, indicating a regulatory role for the identified risk variants. The 40 top genes from the prediction were overrepresented for differential expression in B and T cells according to RNA-sequencing of samples from five healthy donors, with more frequent over-expression in B cells compared to T cells.
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Affiliation(s)
- Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Andrei Alexsson
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lina Sylwan
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Department of Biosciences and Nutrition, Karolinska Institutet, Solna, Sweden
| | - Christofer Bäcklin
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolina Tandre
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska university hospital, Stockholm, Sweden
| | - Christine Bengtsson
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Andreas Jönsen
- Lund University, Skåne University Hospital, Department of Clinical Sciences, Rheumatology, Lund, Sweden
| | | | - Christopher Sjöwall
- AIR/Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Anders A Bengtsson
- Lund University, Skåne University Hospital, Department of Clinical Sciences, Rheumatology, Lund, Sweden
| | - Iva Gunnarsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska university hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska university hospital, Stockholm, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Cai Y, Edin F, Jin Z, Alexsson A, Gudjonsson O, Liu W, Rask-Andersen H, Karlsson M, Li H. Strategy towards independent electrical stimulation from cochlear implants: Guided auditory neuron growth on topographically modified nanocrystalline diamond. Acta Biomater 2016; 31:211-220. [PMID: 26593784 DOI: 10.1016/j.actbio.2015.11.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 12/14/2022]
Abstract
Cochlear implants (CI) have been used for several decades to treat patients with profound hearing loss. Nevertheless, results vary between individuals, and fine hearing is generally poor due to the lack of discrete neural stimulation from the individual receptor hair cells. A major problem is the deliverance of independent stimulation signals to individual auditory neurons. Fine hearing requires significantly more stimulation contacts with intimate neuron/electrode interphases from ordered axonal re-growth, something current CI technology cannot provide. Here, we demonstrate the potential application of micro-textured nanocrystalline diamond (NCD) surfaces on CI electrode arrays. Such textured NCD surfaces consist of micrometer-sized nail-head-shaped pillars (size 5×5μm(2)) made with sequences of micro/nano-fabrication processes, including sputtering, photolithography and plasma etching. The results show that human and murine inner-ear ganglion neurites and, potentially, neural progenitor cells can attach to patterned NCD surfaces without an extracellular matrix coating. Microscopic methods revealed adhesion and neural growth, specifically along the nail-head-shaped NCD pillars in an ordered manner, rather than in non-textured areas. This pattern was established when the inter-NCD pillar distance varied between 4 and 9μm. The findings demonstrate that regenerating auditory neurons show a strong affinity to the NCD pillars, and the technique could be used for neural guidance and the creation of new neural networks. Together with the NCD's unique anti-bacterial and electrical properties, patterned NCD surfaces could provide designed neural/electrode interfaces to create independent electrical stimulation signals in CI electrode arrays for the neural population. STATEMENT OF SIGNIFICANCE Cochlear implant is currently a successful way to treat sensorineural hearing loss and deafness especially in children. Although clinically successful, patients' fine hearing cannot be completely restored. One problem is the amount of the electrodes; 12-20 electrodes are used to replace the function of 3400 inner hair cells. Intense research is ongoing aiming to increase the number of electrodes. This study demonstrates the use of nanocrystalline diamond as a potential nerve-electrode interface. Micrometer-sized nanocrystalline diamond pillars showed high affinity to regenerated human neurons, which grew into a pre-defined network based on the pillar design. Our findings are of particular interest since they can be applied on any silicon-based implant to increase electrode count and to achieve individual neuron stimulation patterns.
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Affiliation(s)
- Yixiao Cai
- Department of Engineering Sciences, Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Edin
- Otolaryngology and Head & Neck Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Zhe Jin
- Physiology; Molecular Physiology and Neuroscience, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Olafur Gudjonsson
- Neurosurgery, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Wei Liu
- Otolaryngology and Head & Neck Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Helge Rask-Andersen
- Otolaryngology and Head & Neck Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Mikael Karlsson
- Department of Engineering Sciences, Ångström Laboratory, Uppsala University, Uppsala, Sweden.
| | - Hao Li
- Otolaryngology and Head & Neck Surgery, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.
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Berggren O, Alexsson A, Morris DL, Tandre K, Weber G, Vyse TJ, Syvanen AC, Ronnblom L, Eloranta ML. IFN- production by plasmacytoid dendritic cell associations with polymorphisms in gene loci related to autoimmune and inflammatory diseases. Hum Mol Genet 2015; 24:3571-81. [DOI: 10.1093/hmg/ddv095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/12/2015] [Indexed: 12/12/2022] Open
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