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Mi J, Wu X, Bai X, Yang Y, Yang H. ST2 and CSF-1 as potential druggable targets of inflammatory bowel diseases: Results from two-sample Mendelian randomization study. Clin Transl Sci 2022; 16:236-245. [PMID: 36333983 PMCID: PMC9926074 DOI: 10.1111/cts.13442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Novel druggable targets are warranted for inflammatory bowel disease (IBD) treatment. We aimed to identify novel circulating proteins with causal associations with the risk of IBDs and provide potential therapeutic targets for IBD treatment. We performed a two-sample Mendelian randomization (MR) study to explore the associations of 55 circulating biomarkers on the risk of IBD, Crohn's disease (CD), and ulcerative colitis (UC) by leveraging the summary statistics from large genomewide association studies and protein quantitative trait loci studies. The individual estimate was pooled together by meta-analyses to estimate the causal effects of each outcome. In univariable MR, we identified several circulating proteins showed potential correlation with IBD, UC, and CD. Of note, we observed that a genetically proxied increased level of suppression of tumorigenicity 2 (ST2) was associated with an elevated risk of IBD (odds ratios [ORs] 1.133, 95% confidence interval [CI] 1.091-1.176, p < 0.0001), CD (ORs 1.188, 95% CI 1.103-1.281, p < 0.0001), and UC cohorts (ORs 1.087, 95% CI 1.050-1.125, p < 0.0001). Additionally, we observed a consistent positive correlation between the level of CSF-1 and the increased risk of IBD in individual MR, with statistically significant causal associations in the meta-analyses with ORs equal to 1.217 (IBD, 95% CI 1.115-1.328, p < 0.0001), 1.223 (CD, 95% CI 1.082-1.382, p = 0.0013), and 1.179 (UC, 95% CI 1.055-1.317, p = 0.0037). This study provided evidence for potential casual associations between circulating ST2 and CSF-1 levels, and increased risks of IBD, UC, and CD, implicating potential treatment targets for IBD and subtypes.
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Affiliation(s)
- Jiarui Mi
- Department of Gastroenterology, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina,Graduate SchoolChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xia Wu
- Department of MedicineTufts Medical CenterMassachusettsBostonUSA
| | - Xiaoyin Bai
- Department of Gastroenterology, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Yang Yang
- Department of Pharmacy, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Hong Yang
- Department of Gastroenterology, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
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2
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Shakerian L, Kolahdooz H, Garousi M, Keyvani V, Kamal Kheder R, Abdulsattar Faraj T, Yazdanpanah E, Esmaeili SA. IL-33/ST2 axis in autoimmune disease. Cytokine 2022; 158:156015. [PMID: 36041312 DOI: 10.1016/j.cyto.2022.156015] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/03/2022]
Abstract
Interleukin-33 (IL-33) is a member of the IL-1 family and plays an ambivalent role in autoimmune diseases. IL-33 signals via the ST2 receptor and drives cytokine production in mast cells, basophils, eosinophils, NK cells, and T lymphocyte cells. The vital role of IL-33 as an active component gives rise to aberrant local and systemic damage which has been demonstrated in numerous inflammatory disorders and immune-mediated pathological conditions including multiple sclerosis (MS), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), psoriasis, Sjogren's syndrome, inflammatory bowel disease (IBD), etc. IL-33/ST2 axis can up-regulate pro-inflammatory cytokine release in autoimmune disease, however, in some metabolic diseases like diabetes mellitus type 1 IL-33 can be considered an anti-inflammatory cytokine. The purpose of this review is to discuss selected studies on IL-33/ST2 axis in autoimmune diseases and its potential role as a pathogenic or protective cytokine.
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Affiliation(s)
- Leila Shakerian
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hanieh Kolahdooz
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mitra Garousi
- Department of Internal Medicine, Faculty of Medical Sciences, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Vahideh Keyvani
- Molecular Genetics, Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Ramiar Kamal Kheder
- Medical Laboratory Science Department, College of Science, University of Raparin, Rania 46012, Sulaymaniyah, Iraq; Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq
| | - Tola Abdulsattar Faraj
- Department of Basic Sciences, College of Medicine, Hawler Medical University, Erbil, Iraq; Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq
| | - Esmaeil Yazdanpanah
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed-Alireza Esmaeili
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Immunology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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3
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Regulation of the Intestinal Extra-Adrenal Steroidogenic Pathway Component LRH-1 by Glucocorticoids in Ulcerative Colitis. Cells 2022; 11:cells11121905. [PMID: 35741034 PMCID: PMC9221003 DOI: 10.3390/cells11121905] [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: 03/28/2022] [Revised: 05/27/2022] [Accepted: 06/08/2022] [Indexed: 02/01/2023] Open
Abstract
Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) and can be treated with glucocorticoids (GC), although some patients are unresponsive to this therapy. The transcription factor LRH-1/NR5A2 is critical to intestinal cortisol production (intestinal steroidogenesis), being reduced in UC patients. However, the relationship between LRH-1 expression and distribution with altered corticosteroid responses is unknown. To address this, we categorized UC patients by their steroid response. Here, we found that steroid-dependent and refractory patients presented reduced glucocorticoid receptor (GR)-mediated intestinal steroidogenesis compared to healthy individuals and responder patients, possibly related to increased colonic mucosa GR isoform beta (GRβ) content and cytoplasmic LRH-1 levels in epithelial and lamina propria cells. Interestingly, an intestinal epithelium-specific GR-induced knockout (GRiKO) dextran sodium sulfate (DSS)-colitis mice model presented decreased epithelial LRH-1 expression, whilst it increased in the lamina propria compared to DSS-treated control mice. Mechanistically, GR directly induced NR5A2 gene expression in CCD841CoN cells and human colonic organoids. Furthermore, GR bound to two glucocorticoid-response elements within the NR5A2 promoter in dexamethasone-stimulated CCD841CoN cells. We conclude that GR contributes to intestinal steroidogenesis by inducing LRH-1 in epithelial cells, suggesting LRH-1 as a potential marker for glucocorticoid-impaired response in UC. However, further studies with a larger patient cohort will be necessary to confirm role of LRH-1 as a therapeutic biomarker.
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Saikumar Jayalatha AK, Hesse L, Ketelaar ME, Koppelman GH, Nawijn MC. The central role of IL-33/IL-1RL1 pathway in asthma: From pathogenesis to intervention. Pharmacol Ther 2021; 225:107847. [PMID: 33819560 DOI: 10.1016/j.pharmthera.2021.107847] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
Interleukin-33 (IL-33), a member of the IL-1 family, and its cognate receptor, Interleukin-1 receptor like-1 (IL-1RL1 or ST2), are susceptibility genes for childhood asthma. In response to cellular damage, IL-33 is released from barrier tissues as an 'alarmin' to activate the innate immune response. IL-33 drives type 2 responses by inducing signalling through its receptor IL-1RL1 in several immune and structural cells, thereby leading to type 2 cytokine and chemokine production. IL-1RL1 gene transcript encodes different isoforms generated through alternative splicing. Its soluble isoform, IL-1RL1-a or sST2, acts as a decoy receptor by sequestering IL-33, thereby inhibiting IL1RL1-b/IL-33 signalling. IL-33 and its receptor IL-1RL1 are therefore considered as putative biomarkers or targets for pharmacological intervention in asthma. This review will provide an overview of the genetics and biology of the IL-33/IL-1RL1 pathway in the context of asthma pathogenesis. It will discuss the potential and complexities of targeting the cytokine or its receptor, how genetics or biomarkers may inform precision medicine for asthma targeting this pathway, and the possible positioning of therapeutics targeting IL-33 or its receptor in the expanding landscape of novel biologicals applied in asthma management.
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Affiliation(s)
- A K Saikumar Jayalatha
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - L Hesse
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - M E Ketelaar
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Beatrix Children's Hospital, Department of Paediatric Pulmonology and Paediatric Allergology, Groningen, the Netherlands
| | - G H Koppelman
- University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Beatrix Children's Hospital, Department of Paediatric Pulmonology and Paediatric Allergology, Groningen, the Netherlands
| | - M C Nawijn
- University of Groningen, University Medical Centre Groningen, Department of Pathology and Medical Biology, Laboratory of Experimental Pulmonology and Inflammation Research (EXPIRE), Groningen, the Netherlands; University of Groningen University Medical Centre Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands.
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6
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Artru F, Bou Saleh M, Maggiotto F, Lassailly G, Ningarhari M, Demaret J, Ntandja-Wandji LC, Pais de Barros JP, Labreuche J, Drumez E, Helou DG, Dharancy S, Gantier E, Périanin A, Chollet-Martin S, Bataller R, Mathurin P, Dubuquoy L, Louvet A. IL-33/ST2 pathway regulates neutrophil migration and predicts outcome in patients with severe alcoholic hepatitis. J Hepatol 2020; 72:1052-1061. [PMID: 31953139 DOI: 10.1016/j.jhep.2019.12.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/30/2019] [Accepted: 12/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Severe alcoholic hepatitis (SAH) is associated with a high risk of infection. The IL-33/ST2 pathway is involved in sepsis control but data regarding its role in alcohol-related liver disease (ALD) are lacking. We aimed to characterize the role of IL-33/ST2 in the polymorphonuclear neutrophils (PMNs) of patients with ALD and SAH. METHODS Serum and circulating neutrophils were collected from patients with SAH, alcoholic cirrhosis and healthy controls. We quantified IL-33/ST2 pathway activity and CXCR2 at baseline and after exposure to IL-33. We also determined the migration capacity of PMNs. RESULTS The decoy receptor of IL-33 (soluble ST2 [sST2]) was increased in SAH vs. cirrhosis and controls, demonstrating the defect in this pathway during ALD. The sST2 level was associated with response to treatment, 2-month survival, infection-free survival and probability of infection in SAH. Endotoxemia was weakly correlated with sST2. GRK2, a negative regulator of CXCR2, was overexpressed in PMNs of patients with SAH and cirrhosis and was decreased by IL-33. CXCR2 levels on PMNs were lower in SAH vs. cirrhosis and controls. Treatment with IL-33 partially restored CXCR2 expression in SAH and cirrhosis. PMN migration upon IL-8 was lower in patients with SAH and cirrhosis vs. controls. Treatment with IL-33 partially restored migration in those with SAH and cirrhosis. Interestingly, the migration capacity of PMNs and the response to IL-33 were enhanced in responders to corticosteroids (Lille <0.45) compared to non-responders. CONCLUSION The IL33/ST2 pathway is defective in SAH and predicts outcome. This defect is associated with decreased CXCR2 expression on the surface of PMNs and lower migration capacity, which can be corrected by IL-33, especially in patients responding to steroids. These results suggest that IL-33 has therapeutic potential for SAH and its infectious complications. LAY SUMMARY The neutrophils of patients with severe alcoholic hepatitis are associated with a defect in the IL-33/ST2 pathway. This defect is associated with lower migration capacities in neutrophils and a higher probability of getting infected. Administration of IL-33 to the neutrophils at least partly restores this defect and may be effective at reducing the risk of infection in patients with severe alcoholic hepatitis.
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Affiliation(s)
- Florent Artru
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Mohamed Bou Saleh
- Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - François Maggiotto
- Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Guillaume Lassailly
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Massih Ningarhari
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Julie Demaret
- Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France; Centre de Biologie-Pathologie, CHU de Lille, Lille, France
| | - Line-Carolle Ntandja-Wandji
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | | | | | - Elodie Drumez
- Département de biostatistiques, CHU de Lille, Lille, France
| | - Doumet Georges Helou
- Inserm/Université Paris-Sud/Université Paris-Saclay, UMR996, Chatenay-Malabry, France; Assistance publique-Hôpitaux de Paris, Hôpital Bichat, Laboratoire d'immunologie « Autoimmunité et Hypersensibilités », Paris, France
| | - Sébastien Dharancy
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Emilie Gantier
- Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Axel Périanin
- Inserm/Faculté de Médecine Xavier Bichat, UMRS-1149, Paris, France; CNRS, ERL-8252 Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France
| | - Sylvie Chollet-Martin
- Inserm/Université Paris-Sud/Université Paris-Saclay, UMR996, Chatenay-Malabry, France; Assistance publique-Hôpitaux de Paris, Hôpital Bichat, Laboratoire d'immunologie « Autoimmunité et Hypersensibilités », Paris, France
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology and Nutrition, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philippe Mathurin
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France
| | - Laurent Dubuquoy
- Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France.
| | - Alexandre Louvet
- Hôpital Claude-Huriez, Service Maladies de l'Appareil Digestif, CHU Lille, Lille, France; Université de Lille/Inserm/CHU de Lille, U995 - LIRIC - Lille Inflammation Research Center, Lille, France.
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Dijk FN, Vijverberg SJ, Hernandez‐Pacheco N, Repnik K, Karimi L, Mitratza M, Farzan N, Nawijn MC, Burchard EG, Engelkes M, Verhamme KM, Potočnik U, Pino‐Yanes M, Postma DS, Maitland‐van der Zee A, Koppelman GH. IL1RL1 gene variations are associated with asthma exacerbations in children and adolescents using inhaled corticosteroids. Allergy 2020; 75:984-989. [PMID: 31755552 PMCID: PMC7176513 DOI: 10.1111/all.14125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- F. Nicole Dijk
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Natalia Hernandez‐Pacheco
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Leila Karimi
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Marianna Mitratza
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Niloufar Farzan
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Martijn C. Nawijn
- Laboratory of Allergology and Pulmonary Diseases, Pathology and Medical Biology Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Esteban G. Burchard
- Department of Medicine University of California San Francisco CA USA
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco CA USA
| | - Marjolein Engelkes
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Katia M. Verhamme
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Maria Pino‐Yanes
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
- CIBER de Enfermedades Respiratorias Instituto de Salud Carlos III Madrid Spain
| | - Dirkje S. Postma
- Department of Pulmonary Diseases Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Anke‐Hilse Maitland‐van der Zee
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy Emma's Children Hospital Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
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8
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Xu Y, Zheng Y, Cao M, Yang W, Ren J, Song Y, Cheng D, Wang J, Huang L, Xu W, Zhao Y, Liu G. Association of Single-Nucleotide Polymorphisms With Chronic Rhinosinusitis in a Southwestern Han Chinese Population: A Replication Study. Am J Rhinol Allergy 2019; 34:352-360. [PMID: 31870168 DOI: 10.1177/1945892419896540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yang Xu
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yongbo Zheng
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Min Cao
- General Affairs Office of Logistic Department, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Yang
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jianjun Ren
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yao Song
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Danni Cheng
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jing Wang
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Ligao Huang
- Department of Otorhinolaryngology, Chengdu Renpin Otorhinolaryngology Hospital, Chengdu, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Yu Zhao
- Department of Otorhinolaryngology Head and Neck Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Geoffrey Liu
- Medical Oncology and Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada.,Medicine and Epidemiology Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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9
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Höglund J, Rafati N, Rask-Andersen M, Enroth S, Karlsson T, Ek WE, Johansson Å. Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers. Sci Rep 2019; 9:16844. [PMID: 31727947 PMCID: PMC6856527 DOI: 10.1038/s41598-019-53111-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.
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Affiliation(s)
- Julia Höglund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Nima Rafati
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Torgny Karlsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Weronica E Ek
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Franco LM, Gadkari M, Howe KN, Sun J, Kardava L, Kumar P, Kumari S, Hu Z, Fraser IDC, Moir S, Tsang JS, Germain RN. Immune regulation by glucocorticoids can be linked to cell type-dependent transcriptional responses. J Exp Med 2019; 216:384-406. [PMID: 30674564 PMCID: PMC6363437 DOI: 10.1084/jem.20180595] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/22/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
A functional genomics approach uncovers previously undescribed cell type–dependent responses that can be linked to the immunoregulatory actions of glucocorticoids in humans. Glucocorticoids remain the most widely used immunosuppressive and anti-inflammatory drugs, yet substantial gaps exist in our understanding of glucocorticoid-mediated immunoregulation. To address this, we generated a pathway-level map of the transcriptional effects of glucocorticoids on nine primary human cell types. This analysis revealed that the response to glucocorticoids is highly cell type dependent, in terms of the individual genes and pathways affected, as well as the magnitude and direction of transcriptional regulation. Based on these data and given their importance in autoimmunity, we conducted functional studies with B cells. We found that glucocorticoids impair upstream B cell receptor and Toll-like receptor 7 signaling, reduce transcriptional output from the three immunoglobulin loci, and promote significant up-regulation of the genes encoding the immunomodulatory cytokine IL-10 and the terminal-differentiation factor BLIMP-1. These findings provide new mechanistic understanding of glucocorticoid action and emphasize the multifactorial, cell-specific effects of these drugs, with potential implications for designing more selective immunoregulatory therapies.
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Affiliation(s)
- Luis M Franco
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Manasi Gadkari
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Katherine N Howe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jing Sun
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Parag Kumar
- Clinical Pharmacokinetics Research Unit, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Sangeeta Kumari
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Zonghui Hu
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Iain D C Fraser
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - John S Tsang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Center for Human Immunology, National Institutes of Health, Bethesda, MD
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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