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Chiñas M, Fernandez-Salinas D, Aguiar VRC, Nieto-Caballero VE, Lefton M, Nigrovic PA, Ermann J, Gutierrez-Arcelus M. Functional genomics implicates natural killer cells as potential key drivers in the pathogenesis of ankylosing spondylitis. medRxiv 2023:2023.09.21.23295912. [PMID: 37808698 PMCID: PMC10557806 DOI: 10.1101/2023.09.21.23295912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Objective Multiple lines of evidence indicate that ankylosing spondylitis (AS) is a lymphocyte-driven disease. However, which lymphocyte populations are critical in AS pathogenesis is not known. In this study, we aimed to identify the key cell types mediating the genetic risk in AS using an unbiased integrative functional genomics approach. Methods We integrated GWAS data with epigenomic and transcriptomic datasets of immune cells in healthy humans. To quantify enrichment of cell type-specific open chromatin regions or gene expression in AS risk loci, we used three published methods which have identified cell types for other diseases. Additionally, we performed co-localization analyses between GWAS risk loci and genetic variants associated with gene expression (eQTL) to find putative target genes of AS risk variants. Results Natural killer (NK) cell-specific open chromatin regions are significantly enriched in heritability for AS, compared to other immune cell types such as T cells, B cells, and monocytes. This finding was consistent between two AS GWAS. Using RNA-seq data, we validated that genes in AS risk loci are enriched in NK cell-specific gene expression. Expression levels of AS-associated genes, such as RUNX3, TBX21, TNFRSF1A, and NPEPPS, were found to be highest in NK cells compared to five T cell subsets. Using the human Space-Time Gut Cell Atlas we found significant upregulation of AS-associated genes predominantly in NK cells. Co-localization analysis revealed four AS risk loci affecting regulation of candidate target genes in NK cells: two known loci, ERAP1 and TNFRSF1A, and two under-studied loci, ENTR1 (aka SDCCAG3) and B3GNT2. Conclusion Our results point to NK cells as potential key drivers in the development of AS and highlight four putative target genes for functional follow-up in NK cells.
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Affiliation(s)
- Marcos Chiñas
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniela Fernandez-Salinas
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Licenciatura en Ciencias Genomicas, Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
| | - Vitor R. C. Aguiar
- Division of Immunology, Boston Children’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
| | - Victor E. Nieto-Caballero
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Licenciatura en Ciencias Genomicas, Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
| | - Micah Lefton
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Peter A. Nigrovic
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Joerg Ermann
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’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
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Bugaj B, Wielińska J, Bogunia-Kubik K, Świerkot J. Searching for New Genetic Biomarkers of Axial Spondyloarthritis. J Clin Med 2022; 11:jcm11102912. [PMID: 35629038 PMCID: PMC9148009 DOI: 10.3390/jcm11102912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Axial spondyloarthritis (axSpA) is a chronic inflammatory condition of the spine. In addition to musculoskeletal symptoms, there are also extra-articular manifestations. The aim of this study was to search for new biomarkers associated with the clinical presentation and treatment response in axSpA patients. Methods: In this study, 106 axSpA patients and 110 healthy controls were enrolled. Six single-nucleotide polymorphisms (SNPs) were selected for genotyping: ERAP1 rs2287987, ERAP2 rs2549782, TNF rs1800629, TNFRSF1A rs767455, TNFRSF1B rs1061622, and FCGR2A rs1801274. Participants were examined at baseline and after 12 and 24 weeks of anti-TNF therapy. Results: SNPs associated with high axSpA initial activity were TNFRSF1A rs767455 and TNFRSF1B rs1061622 (p < 0.008). The ERAP1 rs2287987 AA genotype was more frequently observed in patients with enthesitis (AA vs. G+, p = 0.049), while the TNFRSF1B rs1061622 GG genotype was more common in participants with uveitis (GG vs. TT, p = 0.042). Potential in predicting anti-TNF treatment response was demonstrated by ERAP1 rs2287987, ERAP2 rs2549782, TNFRSF1B rs1061622, and FCGR2A rs1801274. Conclusions: SNPs can be used to identify patients at risk of severe disease to initiate treatment earlier. Genetic testing will allow clinicians to choose the right drug for the patient.
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Affiliation(s)
- Bartosz Bugaj
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
- Correspondence:
| | - Joanna Wielińska
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (J.W.); (K.B.-K.)
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114 Wroclaw, Poland; (J.W.); (K.B.-K.)
| | - Jerzy Świerkot
- Department of Rheumatology and Internal Medicine, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland;
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Sheng N, Gao Y, Li H, Wang W, Geng L, Zhang B, Huang Q, Wang X, Sun L. The Associations of rs1799724 and rs361525 With the Risk of Ankylosing Spondylitis Are Dependent on HLA-B27 Status in a Chinese Han Population. Front Immunol 2022; 13:852326. [PMID: 35450075 PMCID: PMC9016113 DOI: 10.3389/fimmu.2022.852326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Human leucocyte antigen B27 (HLA-B27) is an important biomarker for ankylosing spondylitis (AS). However, delay in the diagnosis of AS is still common in clinical practice. Several single nucleotide polymorphisms (SNPs) in the coding gene of tumor necrosis factor alpha (TNFα) have been reported to be AS susceptibility loci. Our aim was to explore whether SNPs in TNFα could be used to improve the performance of HLA-B27 for predicting AS. Methods Five SNPs (rs1799964, rs1800630, rs1799724, rs1800629, and rs361525) spanning TNFα were genotyped by qPCR-Invader assay in 93 AS patients and 107 healthy controls for association analysis and linkage disequilibrium (LD) analysis. Random forest algorithm was utilized to construct the predictive classifiers for AS. HLA-B was genotyped by PCR-sequence-based typing in a subset of the HLA-B27-positive subjects (38 AS patients and 5 healthy controls). Results The T allele of rs1799724 was verified to significantly increase the risk of AS (OR = 4.583, p < 0.0001), while the A allele of rs361525 showed an association with the reduced AS risk (OR = 0.168, p = 0.009). In addition, the rs1799964T-rs1800630C-rs1799724T-rs1800629G-rs361525G haplotype was significantly associated with a higher risk of AS (p < 0.0001). The optimal set of variables for classifiers to predict AS only consisted of HLA-B27. Strong associations with HLA-B27 status were found in both rs1799724 (p < 0.0001) and rs361525 (p = 0.001), and all the analyzed HLA-B27-positive subjects carried HLA-B*27:04 or HLA-B*27:05. Conclusion In the Chinese Han population, the minor allele T of rs1799724 could increase the risk of AS, while the minor allele A of rs361525 protects individuals from AS. However, the contributions of rs1799724 and rs361525 to AS risk were dependent on HLA-B27 status, suggesting the importance of taking the independence and specificity into consideration in AS susceptibility loci studies.
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Affiliation(s)
- Nan Sheng
- Department of Rheumatology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China.,Clinical Medicine Research Center, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China.,Department of Rheumatology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Yingying Gao
- Department of Rheumatology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Hui Li
- Department of Rheumatology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Wenwen Wang
- Department of Rheumatology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China
| | - Linyu Geng
- Department of Rheumatology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Bo Zhang
- Department of Rheumatology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China
| | - Qiang Huang
- State Key Laboratory of Environmental Geochemistry Institute of Geochemistry, Chinese Academy of Science, Guiyang, China
| | - Xueqin Wang
- Department of Rheumatology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, China
| | - Lingyun Sun
- Department of Rheumatology, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
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Ortolan A, Cozzi G, Lorenzin M, Galozzi P, Doria A, Ramonda R. The Genetic Contribution to Drug Response in Spondyloarthritis: A Systematic Literature Review. Front Genet 2021; 12:703911. [PMID: 34354741 PMCID: PMC8329488 DOI: 10.3389/fgene.2021.703911] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 05/01/2021] [Accepted: 06/21/2021] [Indexed: 01/28/2023] Open
Abstract
Objective: Spondyloarthritis (SpA) are a group of diseases with a high heritability, whose pathogenesis is strongly determined by an interplay between genetic and environmental factor. Therefore, the aim of our study was to determine whether genetic variants could also influence response to therapy in SpA. Methods: A systematic literature review (SLR) was conducted in PubMed and Web of Science core collection, without publication-year restrictions (Last search 8th April 2021). The search strategy was formulated according to the PEO format (Population, Exposure, Outcome) for observational studies. The population was adult (≥18 years) patients with SpA. The exposure was inheritable genetic variations of any gene involved in the disease pathogenesis/drug metabolism. The outcome was response to the drug, both as dichotomous (response yes/no) and as continuous outcomes. Exclusion criteria were: (1) languages other than English, (2) case series, case reports, editorials, and reviews, (3) studies reporting genetic contribution to drug response only limited to extra-musculoskeletal features of SpA, (4) epigenetic modifications. Quality of the included study was independently assessed by two authors. Results: After deduplication, 393 references were screened by two authors, which led to the final inclusion of 26 articles, pertinent with the research question, that were considered for qualitative synthesis. Among these, 10 cohort, one cross-sectional, and five case-control studies were considered of at least good quality according to Newcastle-Ottawa Scale (NOS). In studies about TNF-blockers therapy: (1) polymorphisms of the TNF receptor superfamily 1A/1B (TNFRSF1A/1B) genes were most frequently able to predict response, (2) -238 and -308 polymorphisms of TNFα gene were studied with conflicting results, (3) TNFα polymorphism rs1799724, rs1799964, -857, -1,013, +489 predicted drug response in non-adjusted analysis, (4) PDE3A rs3794271 had a linear relationship with DAS28 reduction after anti-TNFα therapy. DHFR polymorphism +35,289 was able to predict response to methotrexate. Conclusions: Our SLR highlighted the existence of a genetic component in determining drug response. However, further studies are warranted to better define quantify it.
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Affiliation(s)
- Augusta Ortolan
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
| | - Giacomo Cozzi
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
| | - Mariagrazia Lorenzin
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
| | - Paola Galozzi
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine DIMED, University of Padova, Padua, Italy
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Xu Y, Jiang W, Zhang H. Association between C-reactive protein gene variant and treatment efficacy of etanercept in ankylosing spondylitis patients receiving hip arthroplasty. J Clin Lab Anal 2020; 34:e23343. [PMID: 32311164 PMCID: PMC7439327 DOI: 10.1002/jcla.23343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/21/2020] [Accepted: 03/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND C-reactive protein (CRP) level is one of the most widely used parameters to assess ankylosing spondylitis (AS), since CRP is associated with poor radiographic progression of AS patients. Recent studies have investigated the association between CRP gene variants and AS risk, but with conflicting findings. MATERIAL AND METHODS We enrolled 232 AS cases and 314 controls in this case-control study. Next, we assessed the association of CRP gene rs3091244 polymorphism with the efficacy of etanercept for AS. Genotyping was done using a custom-by-design 48-Plex SNP scanTM Kit. RESULTS CRP gene rs3091244 polymorphism was associated with an increased risk of AS in this Chinese population. Clinical indicators of AS patients including morning stiffness time, Bath AS function index (BASFI), Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Visual Analogue Scale (VAS), erythrocyte sedimentation rate (ESR), and CRP were significantly decreased after 12 weeks of etanercept treatment. Furthermore, AA genotype carriers showed higher values of VAS, BASDAI, BASFI, and CRP before etanercept treatment. AA genotype or A allele of rs3091244 polymorphism was associated with Ankylosing Spondylitis Assessment Study group response criteria 20 scores (ASAS20) and Assessment in SpondyloArthritis international Society 40 response (ASAS40) improvement. In addition, AA genotype carriers showed significantly higher CRP levels compared with genotype GG carriers (16.3 vs 8.8 mg/L). CONCLUSION CRP gene rs3091244 polymorphism is associated with an increased risk of AS. Additionally, rs3091244 polymorphism could serve as a biomarker for good response to etanercept treatment in AS.
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Affiliation(s)
- Yuansheng Xu
- Department of Orthopedics, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wei Jiang
- Department of Orthopedics, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Hui Zhang
- Department of Orthopedics, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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Nii T, Kuzuya K, Kabata D, Matsui T, Murata A, Ohya T, Matsuoka H, Shimizu T, Oguro E, Okita Y, Udagawa C, Yoshimura M, Kudo-Tanaka E, Teshigawara S, Harada Y, Yoshida Y, Isoda K, Tsuji SI, Ohshima S, Hashimoto J, Shintani A, Takehana Y, Tohma S, Saeki Y. Crosstalk between tumor necrosis factor-alpha signaling and aryl hydrocarbon receptor signaling in nuclear factor –kappa B activation: A possible molecular mechanism underlying the reduced efficacy of TNF-inhibitors in rheumatoid arthritis by smoking. J Autoimmun 2019; 98:95-102. [DOI: 10.1016/j.jaut.2018.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 12/15/2022]
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