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Bhuyan ZA, Rahman MA, Maradana MR, Mehdi AM, Bergot AS, Simone D, El-Kurdi M, Garrido-Mesa J, Cai CBB, Cameron AJ, Hanson AL, Nel HJ, Kenna T, Leo P, Rehaume L, Brown MA, Ciccia F, Thomas R. Genetically encoded Runx3 and CD4 + intestinal epithelial lymphocyte deficiencies link SKG mouse and human predisposition to spondyloarthropathy. Clin Immunol 2023; 247:109220. [PMID: 36596403 DOI: 10.1016/j.clim.2022.109220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/02/2023]
Abstract
Disturbances in immune regulation, intestinal dysbiosis and inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. In small intestine, Foxp3+ regulatory T cells (Treg) and CD4+CD8αα+TCRαβ+ intraepithelial lymphocytes (CD4-IEL) control inflammation. TGF-β and retinoic acid (RA)-producing dendritic cells and MHC-class II+ intestinal epithelial cells (IEC) are required for Treg and CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We show in SKG mouse ileum, that ZAP70W163C or ZAP70 inhibition prevented CD4-IEL but not Treg differentiation, dysregulating Runx3 and ThPOK. TGF-β/RA-mediated CD4-IEL development, T-cell IFN-γ production, MHC class-II+ IEC, tissue-resident memory T-cell and Runx3-regulated genes were reduced. In AS intestine, CD4-IEL were decreased, while in AS blood CD4+CD8+ T cells were reduced and Treg increased. Thus, genetically-encoded TCR signaling dysfunction links intestinal T-cell immunodeficiency in mouse and human spondyloarthropathy.
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Affiliation(s)
- Zaied Ahmed Bhuyan
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - M Arifur Rahman
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Muralidhara Rao Maradana
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Anne-Sophie Bergot
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Davide Simone
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marya El-Kurdi
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheng Bang Benjamin Cai
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Amy J Cameron
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Aimee L Hanson
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Hendrik J Nel
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Tony Kenna
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Paul Leo
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Linda Rehaume
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Genomics England Ltd, Charterhouse Square, London, United Kingdom
| | - Francesco Ciccia
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Ranjeny Thomas
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
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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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Coassin S, Hermann-Kleiter N, Haun M, Wahl S, Wilson R, Paulweber B, Kunze S, Meitinger T, Strauch K, Peters A, Waldenberger M, Kronenberg F, Lamina C. A genome-wide analysis of DNA methylation identifies a novel association signal for Lp(a) concentrations in the LPA promoter. PLoS One 2020; 15:e0232073. [PMID: 32343731 PMCID: PMC7188291 DOI: 10.1371/journal.pone.0232073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/19/2020] [Indexed: 12/24/2022] Open
Abstract
Lipoprotein(a) [Lp(a)] is a major cardiovascular risk factor, which is largely genetically determined by one major gene locus, the LPA gene. Many aspects of the transcriptional regulation of LPA are poorly understood and the role of epigenetics has not been addressed yet. Therefore, we conducted an epigenome-wide analysis of DNA methylation on Lp(a) levels in two population-based studies (total n = 2208). We identified a CpG site in the LPA promoter which was significantly associated with Lp(a) concentrations. Surprisingly, the identified CpG site was found to overlap the SNP rs76735376. We genotyped this SNP de-novo in three studies (total n = 7512). The minor allele of rs76735376 (1.1% minor allele frequency) was associated with increased Lp(a) values (p = 1.01e-59) and explained 3.5% of the variation of Lp(a). Statistical mediation analysis showed that the effect on Lp(a) is rather originating from the base change itself and is not mediated by DNA methylation levels. This finding is supported by eQTL data from 208 liver tissue samples from the GTEx project, which shows a significant association of the rs76735376 minor allele with increased LPA expression. To evaluate, whether the association signal at rs76735376 may actually be derived from a stronger eQTL signal in LD with this SNP, eQTL association results of all correlated SNPs (r2≥0.1) were integrated with genetic association results. This analysis pinpointed to rs10455872 as the potential trigger of the effect of rs76735376. Furthermore, both SNPs coincide with short apo(a) isoforms. Adjusting for both, rs10455872 and the apo(a) isoforms diminished the effect size of rs76735376 to 5.38 mg/dL (p = 0.0463). This indicates that the effect of rs76735376 can be explained by both an independent effect of the SNP and a strong correlation with rs10455872 and apo(a) isoforms.
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Affiliation(s)
- Stefan Coassin
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Natascha Hermann-Kleiter
- Department of Genetics and Pharmacology, Institute of Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Margot Haun
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University, Salzburg, Austria
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- German Research Center for Environmental Health, Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Konstantin Strauch
- German Research Center for Environmental Health, Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Claudia Lamina
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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Identification of Candidate Genes Related to Inflammatory Bowel Disease Using Minimum Redundancy Maximum Relevance, Incremental Feature Selection, and the Shortest-Path Approach. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5741948. [PMID: 28293637 PMCID: PMC5331171 DOI: 10.1155/2017/5741948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/11/2017] [Indexed: 02/08/2023]
Abstract
Identification of disease genes is a hot topic in biomedicine and genomics. However, it is a challenging problem because of the complexity of diseases. Inflammatory bowel disease (IBD) is an idiopathic disease caused by a dysregulated immune response to host intestinal microflora. It has been proven to be associated with the development of intestinal malignancies. Although the specific pathological characteristics and genetic background of IBD have been partially revealed, it is still an overdetermined disease and the blueprint of all genetic variants still needs to be improved. In this study, a novel computational method was built to identify genes related to IBD. Samples from two subtypes of IBD (ulcerative colitis and Crohn's disease) and normal samples were employed. By analyzing the gene expression profiles of these samples using minimum redundancy maximum relevance and incremental feature selection, 21 genes were obtained that could effectively distinguish samples from the two subtypes of IBD and the normal samples. Then, the shortest-path approach was used to search for an additional 20 genes in a large network constructed using protein-protein interactions based on the above-mentioned 21 genes. Analyses of the 41 genes obtained indicate that they are closely associated with this disease.
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NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia. PLoS One 2017; 12:e0171164. [PMID: 28151996 PMCID: PMC5289504 DOI: 10.1371/journal.pone.0171164] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) cells represent developmentally arrested T-cell progenitors, subsets of which aberrantly express homeobox genes of the NKL subclass, including TLX1, TLX3, NKX2-1, NKX2-5, NKX3-1 and MSX1. Here, we analyzed the transcriptional landscape of all 48 members of the NKL homeobox gene subclass in CD34+ hematopoietic stem and progenitor cells (HSPCs) and during lymphopoiesis, identifying activities of nine particular genes. Four of these were expressed in HSPCs (HHEX, HLX1, NKX2-3 and NKX3-1) and three in common lymphoid progenitors (HHEX, HLX1 and MSX1). Interestingly, our data indicated downregulation of NKL homeobox gene transcripts in late progenitors and mature T-cells, a phenomenon which might explain the oncogenic impact of this group of genes in T-ALL. Using MSX1-expressing T-ALL cell lines as models, we showed that HHEX activates while HLX1, NKX2-3 and NKX3-1 repress MSX1 transcription, demonstrating the mutual regulation and differential activities of these homeobox genes. Analysis of a public T-ALL expression profiling data set comprising 117 patient samples identified 20 aberrantly activated members of the NKL subclass, extending the number of known NKL homeobox oncogene candidates. While 7/20 genes were also active during hematopoiesis, the remaining 13 showed ectopic expression. Finally, comparative analyses of T-ALL patient and cell line profiling data of NKL-positive and NKL-negative samples indicated absence of shared target genes but instead highlighted deregulation of apoptosis as common oncogenic effect. Taken together, we present a comprehensive survey of NKL homeobox genes in early hematopoiesis, T-cell development and T-ALL, showing that these genes generate an NKL-code for the diverse stages of lymphoid development which might be fundamental for regular differentiation.
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Chillappagari S, Venkatesan S, Garapati V, Mahavadi P, Munder A, Seubert A, Sarode G, Guenther A, Schmeck BT, Tümmler B, Henke MO. Impaired TLR4 and HIF expression in cystic fibrosis bronchial epithelial cells downregulates hemeoxygenase-1 and alters iron homeostasis in vitro. Am J Physiol Lung Cell Mol Physiol 2014; 307:L791-9. [DOI: 10.1152/ajplung.00167.2014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hemeoxygenase-1 (HO-1), an inducible heat shock protein, is upregulated in response to multiple cellular insults via oxidative stress, lipopolysaccharides (LPS), and hypoxia. In this study, we investigated in vitro the role of Toll-like receptor 4 (TLR4), hypoxia-inducible factor 1α (HIF-1α), and iron on HO-1 expression in cystic fibrosis (CF). Immunohistochemical analysis of TLR4, HO-1, ferritin, and HIF-1α were performed on lung sections of CFTR−/− and wild-type mice. CFBE41o- and 16HBE14o- cell lines were employed for in vitro analysis via immunoblotting, immunofluorescence, real-time PCR, luciferase reporter gene analysis, and iron quantification. We observed a reduced TLR4, HIF-1α, HO-1, and ferritin in CFBE41o- cell line and CF mice. Knockdown studies using TLR4-siRNA in 16HBE14o- revealed significant decrease of HO-1, confirming the role of TLR4 in HO-1 downregulation. Inhibition of HO-1 using tin protoporphyrin in 16HBE14o- cells resulted in increased iron levels, suggesting a probable role of HO-1 in iron accumulation. Additionally, sequestration of excess iron using iron chelators resulted in increased hypoxia response element response in CFBE41o- and 16HBE14o-, implicating a role of iron in HIF-1α stabilization and HO-1. To conclude, our in vitro results demonstrate that multiple regulatory factors, such as impaired TLR4 surface expression, increased intracellular iron, and decreased HIF-1α, downregulate HO-1 expression in CFBE41o- cells.
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Affiliation(s)
- Shashi Chillappagari
- Department of Medicine, Pulmonary Critical Care Philipps University, Marburg, Germany
- Institute for Lung Research, Philipps-University, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Shalini Venkatesan
- Department of Internal Medicine, Justus-Liebig-University, Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Virajith Garapati
- Department of Medicine, Pulmonary Critical Care Philipps University, Marburg, Germany
- Institute for Lung Research, Philipps-University, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Poornima Mahavadi
- Department of Internal Medicine, Justus-Liebig-University, Giessen, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Antje Munder
- Clinical Research Group ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’, Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Germany
| | - Andreas Seubert
- Department of Chemistry-Biochemistry, Philipps University, Marburg, Germany
| | - Gaurav Sarode
- Department of Medicine, Pulmonary Critical Care Philipps University, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Justus-Liebig-University, Giessen, Germany
- Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Bernd T. Schmeck
- Institute for Lung Research, Philipps-University, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
| | - Burkhard Tümmler
- Clinical Research Group ‘Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics’, Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Germany
| | - Markus O. Henke
- Department of Medicine, Pulmonary Critical Care Philipps University, Marburg, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
- Member of the German Center for Lung Research (DZL)
- Pneumology, Asklepios Fachkliniken München-Gauting, Germany
- Comprehensive Pneumology Center (CPC), Helmholtz Zentrum, Munich, Germany
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Contribution of NKX2-3 polymorphisms to inflammatory bowel diseases: a meta-analysis of 35358 subjects. Sci Rep 2014; 4:3924. [PMID: 24473197 PMCID: PMC5379238 DOI: 10.1038/srep03924] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/13/2014] [Indexed: 02/07/2023] Open
Abstract
Polymorphisms in NKX2-3 gene have been inconsistently associated with Crohn's disease (CD) and ulcerative colitis (UC). To generate large-scale evidence on whether NKX2-3 polymorphisms are associated with CD or UC susceptibility we have conducted a meta-analysis of 17 studies involving 17329 patients and 18029 controls. A significantly increased CD or UC risk was observed in persons carrying a G allele at rs10883365 polymorphism (A/G) compared with those with a A allele. (OR = 1.226, 95%CI: 1.177–1.277 and OR = 1.274, 95%CI: 1.175–1.382 respectively). In the subgroup analysis, a significantly increased CD risk was found in both Europeans and Asians. For rs11190140 polymorphism (C/T) and CD risk, the risk estimate for the allele contrast was OR = 1.201 (1.136–1.269). This meta-analysis provided a robust result that persons with a G or T allele may have a moderately increased risk of CD, and suggested that rs10883365 polymorphism was also a candidate gene polymorphism for UC susceptibility.
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Pan MG, Xiong Y, Chen F. NFAT gene family in inflammation and cancer. Curr Mol Med 2013; 13:543-54. [PMID: 22950383 DOI: 10.2174/1566524011313040007] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 08/04/2012] [Accepted: 08/10/2012] [Indexed: 01/28/2023]
Abstract
Calcineurin-NFAT signaling is critical for numerous aspects of vertebrate function during and after embryonic development. Initially discovered in T cells, the NFAT gene family, consisting of five members, regulates immune system, inflammatory response, angiogenesis, cardiac valve formation, myocardial development, axonal guidance, skeletal muscle development, bone homeostasis, development and metastasis of cancer, and many other biological processes. In this review we will focus on the NFAT literature relevant to the two closely related pathological systems: inflammation and cancer.
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Affiliation(s)
- M-G Pan
- Division of Oncology and Hematology, Kaiser Permanente Medical Center, Santa Clara, CA 95051, USA.
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Abstract
BACKGROUND A large-scale meta-analysis of a series of European genome-wide association studies revealed 71 susceptibility loci for Crohn's disease (CD). However, it is not clear whether these susceptibility loci are also shared with Japanese populations. METHODS We genotyped 71 single-nucleotide polymorphisms (SNPs) comprising 1311 CD cases and 6585 controls of Japanese descent, and their associations with CD were evaluated using the Cochran-Armitage trend test. In addition, genotype-phenotype analyses were conducted on the SNPs showing associations with Japanese CD based on the Montreal classification. RESULTS Twenty-seven SNPs showed at least nominal association (P < 0.05) and 11 of them remained significant even after Bonferroni correction (P < 0.0007). Despite high statistical power, we could not find any association in 17 loci. Moreover, SNPs in 9 loci were rare or absent in the Japanese population. Genetic variations involved in the innate immune system (NOD2, ATG16L1, and IRGM) showed no association with CD susceptibility in the Japanese population. Genotype-phenotype analyses showed that rs3810936, a marker of TNFSF15, correlated with severe CD phenotypes. CONCLUSIONS Our study suggests that there is a differential genetic background of CD susceptibility between Japanese and European populations.
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Sirohi S, Bakalkin G, Walker BM. Alcohol-induced plasticity in the dynorphin/kappa-opioid receptor system. Front Mol Neurosci 2012; 5:95. [PMID: 23060746 PMCID: PMC3459013 DOI: 10.3389/fnmol.2012.00095] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 08/29/2012] [Indexed: 01/02/2023] Open
Abstract
Alcoholism is a chronic relapsing disorder characterized by continued alcohol use despite numerous adverse consequences. Alcohol has been shown to interact with numerous neurotransmitter systems to exert its pharmacological effects. The endogenous opioid system (EOS) has been strongly implicated in the positive and negative reinforcing effects of alcohol. Traditionally recognized as dysphoric/anhedonic in nature, the dynorphin/kappa-opioid receptor (DYN/KOR) system has recently received considerable attention due to evidence suggesting that an upregulated DYN/KOR system may be a critical contributor to the complex factors that result in escalated alcohol consumption once dependent. The present review will discuss alcohol-induced plasticity in the DYN/KOR system and how these neuroadaptations could contribute to excessive alcohol seeking and consumption.
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Affiliation(s)
- Sunil Sirohi
- Laboratory of Alcoholism and Addictions Neuroscience, Department of Psychology, Washington State University Pullman, WA, USA
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Neuman MG, Nanau RM. Single-nucleotide polymorphisms in inflammatory bowel disease. Transl Res 2012; 160:45-64. [PMID: 22687962 DOI: 10.1016/j.trsl.2011.10.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 12/23/2022]
Abstract
Strong evidence indicates that inflammatory bowel disease, including Crohn disease and ulcerative colitis, is a result of an inappropriate inflammatory response in which genetic and environmental factors play important roles. This review discusses several single-nucleotide polymorphisms with either susceptibility or protective effects on inflammatory bowel disease.
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Affiliation(s)
- Manuela G Neuman
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, and In Vitro Drug Safety and Biotechnology, MaRS, Toronto, Ontario, Canada.
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