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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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Abstract
T lymphocytes undergo carefully orchestrated programming during development in the thymus and subsequently during differentiation in the periphery. This intricate specification allows for cell-type and context-specific transcriptional programs that regulate immune responses to infection and malignancy. Epigenetic changes, including histone modifications and covalent modification of DNA itself through DNA methylation, are now recognized to play a critical role in these cell-fate decisions. DNA methylation is mediated primarily by the actions of the DNA methyltransferase (DNMT) and ten-eleven-translocation (TET) families of epigenetic enzymes. In this review, we discuss the role of DNA methylation and its enzymatic regulators in directing the development and differentiation of CD4+ and CD8+ T-cells.
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Affiliation(s)
- Luis O Correa
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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3
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Bezu L, Wu Chuang A, Liu P, Kroemer G, Kepp O. Immunological Effects of Epigenetic Modifiers. Cancers (Basel) 2019; 11:cancers11121911. [PMID: 31805711 PMCID: PMC6966579 DOI: 10.3390/cancers11121911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/23/2022] Open
Abstract
Epigenetic alterations are associated with major pathologies including cancer. Epigenetic dysregulation, such as aberrant histone acetylation, altered DNA methylation, or modified chromatin organization, contribute to oncogenesis by inactivating tumor suppressor genes and activating oncogenic pathways. Targeting epigenetic cancer hallmarks can be harnessed as an immunotherapeutic strategy, exemplified by the use of pharmacological inhibitors of DNA methyltransferases (DNMT) and histone deacetylases (HDAC) that can result in the release from the tumor of danger-associated molecular patterns (DAMPs) on one hand and can (re-)activate the expression of tumor-associated antigens on the other hand. This finding suggests that epigenetic modifiers and more specifically the DNA methylation status may change the interaction of chromatin with chaperon proteins including HMGB1, thereby contributing to the antitumor immune response. In this review, we detail how epigenetic modifiers can be used for stimulating therapeutically relevant anticancer immunity when used as stand-alone treatments or in combination with established immunotherapies.
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Affiliation(s)
- Lucillia Bezu
- Service anesthésie-réanimation, Hôpital européen Georges Pompidou, AP-HP, 75015 Paris, France;
- Faculty of Medicine, University of Paris Sud, 94270 Kremlin-Bicêtre, France;
- Equipe labellisée par la Ligue contre le cancer, 75000, Paris, France;
- Université de Paris, Sorbonne, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
| | - Alejandra Wu Chuang
- Faculty of Medicine, University of Paris Sud, 94270 Kremlin-Bicêtre, France;
- Equipe labellisée par la Ligue contre le cancer, 75000, Paris, France;
- Université de Paris, Sorbonne, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
| | - Peng Liu
- Equipe labellisée par la Ligue contre le cancer, 75000, Paris, France;
- Université de Paris, Sorbonne, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
| | - Guido Kroemer
- Equipe labellisée par la Ligue contre le cancer, 75000, Paris, France;
- Université de Paris, Sorbonne, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, 215123 Suzhou, China
- Department of Women’s and Children’s Health, Karolinska Institute, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Correspondence: (G.K.); (O.K.)
| | - Oliver Kepp
- Equipe labellisée par la Ligue contre le cancer, 75000, Paris, France;
- Université de Paris, Sorbonne, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France
- Correspondence: (G.K.); (O.K.)
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Yang IV, Konigsberg I, MacPhail K, Li L, Davidson EJ, Mroz PM, Hamzeh N, Gillespie M, Silveira LJ, Fingerlin TE, Maier LA. DNA Methylation Changes in Lung Immune Cells Are Associated with Granulomatous Lung Disease. Am J Respir Cell Mol Biol 2019; 60:96-105. [PMID: 30141971 DOI: 10.1165/rcmb.2018-0177oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Epigenetic marks are likely to explain variability of response to antigen in granulomatous lung disease. The objective of this study was to identify DNA methylation and gene expression changes associated with chronic beryllium disease (CBD) and sarcoidosis in lung cells obtained by BAL. BAL cells from CBD (n = 8), beryllium-sensitized (n = 8), sarcoidosis (n = 8), and additional progressive sarcoidosis (n = 9) and remitting (n = 15) sarcoidosis were profiled on the Illumina 450k methylation and Affymetrix/Agilent gene expression microarrays. Statistical analyses were performed to identify DNA methylation and gene expression changes associated with CBD, sarcoidosis, and disease progression in sarcoidosis. DNA methylation array findings were validated by pyrosequencing. We identified 52,860 significant (P < 0.005 and q < 0.05) CpGs associated with CBD; 2,726 CpGs near 1,944 unique genes have greater than 25% methylation change. A total of 69% of differentially methylated genes are significantly (q < 0.05) differentially expressed in CBD, with many canonical inverse relationships of methylation and expression in genes critical to T-helper cell type 1 differentiation, chemokines and their receptors, and other genes involved in immunity. Testing of these CBD-associated CpGs in sarcoidosis reveals that methylation changes only approach significance, but are methylated in the same direction, suggesting similarities between the two diseases with more heterogeneity in sarcoidosis that limits power with the current sample size. Analysis of progressive versus remitting sarcoidosis identified 15,215 CpGs (P < 0.005 and q < 0.05), but only 801 of them have greater than 5% methylation change, demonstrating that DNA methylation marks of disease progression changes are more subtle. Our study highlights the significance of epigenetic marks in lung immune response in granulomatous lung disease.
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Affiliation(s)
- Ivana V Yang
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,2 Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado.,3 Center for Genes, Environment, and Health
| | - Iain Konigsberg
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | | | - Li Li
- 4 Department of Medicine, and
| | - Elizabeth J Davidson
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | | | | | | | | | - Tasha E Fingerlin
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,3 Center for Genes, Environment, and Health.,5 Department of Biomedical Research, National Jewish Health, Denver, Colorado; and.,6 Department of Biostatistics and Bioinformatics and
| | - Lisa A Maier
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,4 Department of Medicine, and.,7 Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, Colorado
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Ahlén Bergman E, Hartana CA, Johansson M, Linton LB, Berglund S, Hyllienmark M, Lundgren C, Holmström B, Palmqvist K, Hansson J, Alamdari F, Huge Y, Aljabery F, Riklund K, Winerdal ME, Krantz D, Zirakzadeh AA, Marits P, Sjöholm LK, Sherif A, Winqvist O. Increased CD4 + T cell lineage commitment determined by CpG methylation correlates with better prognosis in urinary bladder cancer patients. Clin Epigenetics 2018; 10:102. [PMID: 30075815 PMCID: PMC6076404 DOI: 10.1186/s13148-018-0536-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/24/2018] [Indexed: 12/24/2022] Open
Abstract
Background Urinary bladder cancer is a common malignancy worldwide. Environmental factors and chronic inflammation are correlated with the disease risk. Diagnosis is performed by transurethral resection of the bladder, and patients with muscle invasive disease preferably proceed to radical cystectomy, with or without neoadjuvant chemotherapy. The anti-tumour immune responses, known to be initiated in the tumour and draining lymph nodes, may play a major role in future treatment strategies. Thus, increasing the knowledge of tumour-associated immunological processes is important. Activated CD4+ T cells differentiate into four main separate lineages: Th1, Th2, Th17 and Treg, and they are recognized by their effector molecules IFN-γ, IL-13, IL-17A, and the transcription factor Foxp3, respectively. We have previously demonstrated signature CpG sites predictive for lineage commitment of these four major CD4+ T cell lineages. Here, we investigate the lineage commitment specifically in tumour, lymph nodes and blood and relate them to the disease stage and response to neoadjuvant chemotherapy. Results Blood, tumour and regional lymph nodes were obtained from patients at time of transurethral resection of the bladder and at radical cystectomy. Tumour-infiltrating CD4+ lymphocytes were significantly hypomethylated in all four investigated lineage loci compared to CD4+ lymphocytes in lymph nodes and blood (lymph nodes vs tumour-infiltrating lymphocytes: IFNG -4229 bp p < 0.0001, IL13 -11 bp p < 0.05, IL17A -122 bp p < 0.01 and FOXP3 -77 bp p > 0.05). Examination of individual lymph nodes displayed different methylation signatures, suggesting possible correlation with future survival. More advanced post-cystectomy tumour stages correlated significantly with increased methylation at the IFNG -4229 bp locus. Patients with complete response to neoadjuvant chemotherapy displayed significant hypomethylation in CD4+ T cells for all four investigated loci, most prominently in IFNG p < 0.0001. Neoadjuvant chemotherapy seemed to result in a relocation of Th1-committed CD4+ T cells from blood, presumably to the tumour, indicated by shifts in the methylation patterns, whereas no such shifts were seen for lineages corresponding to IL13, IL17A and FOXP3. Conclusion Increased lineage commitment in CD4+ T cells, as determined by demethylation in predictive CpG sites, is associated with lower post-cystectomy tumour stage, complete response to neoadjuvant chemotherapy and overall better outcome, suggesting epigenetic profiling of CD4+ T cell lineages as a useful readout for clinical staging. Electronic supplementary material The online version of this article (10.1186/s13148-018-0536-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emma Ahlén Bergman
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Ciputra Adijaya Hartana
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Markus Johansson
- Department of Urology, Sundsvall Hospital, Sundsvall, Sweden.,Department of surgical and perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Ludvig B Linton
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sofia Berglund
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Christian Lundgren
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Benny Holmström
- Department of Urology, Akademiska University Hospital, Uppsala, Sweden
| | - Karin Palmqvist
- Department of surgical and perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden.,Department of Surgery, Urology Section, Östersund County Hospital, Östersund, Sweden
| | - Johan Hansson
- Centre for Research and Development, Faculty of Medicine, Uppsala University, County Council of Gävleborg, Uppsala, Sweden
| | | | - Ylva Huge
- Department of Clinical and Experimental Medicine, Division of Urology, Linköping University, Linköping, Sweden
| | - Firas Aljabery
- Department of Clinical and Experimental Medicine, Division of Urology, Linköping University, Linköping, Sweden
| | - Katrine Riklund
- Department of Radiation Sciences, Diagnostic Radiology, Umeå University, Umeå, Sweden
| | - Malin E Winerdal
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Krantz
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - A Ali Zirakzadeh
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of surgical and perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | - Per Marits
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Louise K Sjöholm
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Amir Sherif
- Department of surgical and perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden.,Department of Radiation Sciences, Diagnostic Radiology, Umeå University, Umeå, Sweden
| | - Ola Winqvist
- Unit of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Yang IV, Richards A, Davidson EJ, Stevens AD, Kolakowski CA, Martin RJ, Schwartz DA. The Nasal Methylome: A Key to Understanding Allergic Asthma. Am J Respir Crit Care Med 2017; 195:829-831. [PMID: 28294656 DOI: 10.1164/rccm.201608-1558le] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ivana V Yang
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
| | - Adam Richards
- 1 University of Colorado School of Medicine Aurora, Colorado and
| | | | | | | | - Richard J Martin
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
| | - David A Schwartz
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
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Martin LJ, He H, Collins MH, Abonia JP, Biagini Myers JM, Eby M, Johansson H, Kottyan LC, Khurana Hershey GK, Rothenberg ME. Eosinophilic esophagitis (EoE) genetic susceptibility is mediated by synergistic interactions between EoE-specific and general atopic disease loci. J Allergy Clin Immunol 2017; 141:1690-1698. [PMID: 29129581 DOI: 10.1016/j.jaci.2017.09.046] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/26/2017] [Accepted: 09/27/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is an esophageal inflammatory disease associated with atopic diseases. Thymic stromal lymphopoietin (TSLP) and calpain 14 (CAPN14) genetic variations contribute to EoE, but how this relates to atopy is unclear. OBJECTIVE The purpose of this study was to explore the relationship between EoE, atopy, and genetic risk. METHODS EoE-atopy enrichment was tested by using 700 patients with EoE and 801 community control subjects. Probing 372 single nucleotide polymorphisms (SNPs) in 63 atopy genes, we evaluated EoE associations using 412 nonatopic and 868 atopic disease control subjects. Interaction and stratified analyses of EoE-specific and atopy-related SNPs were performed. RESULTS Atopic disease was enriched in patients with EoE (P < .0001). Comparing patients with EoE and nonatopic control subjects, EoE associated strongly with IL-4/kinesin family member 3A (IL4/KIF3A) (P = 2.8 × 10-6; odds ratio [OR], 1.87), moderately with TSLP (P = 1.5 × 10-4; OR, 1.43), and nominally with CAPN14 (P = .029; OR, 1.35). Comparing patients with EoE with atopic disease control subjects, EoE associated strongly with ST2 (P = 3.5 × 10-6; OR, 1.77) and nominally with IL4/KIF3A (P = .019; OR, 1.25); TSLP's association persisted (P = 4.7 × 10-5; OR, 1.37), and CAPN14's association strengthened (P = .0001; OR, 1.71). Notably, there was gene-gene interaction between TSLP and IL4 SNPs (P = .0074). Children with risk alleles for both genes were at higher risk for EoE (P = 2.0 × 10-10; OR, 3.67). CONCLUSIONS EoE genetic susceptibility is mediated by EoE-specific and general atopic disease loci, which can have synergistic effects. These results might aid in identifying potential therapeutics and predicting EoE susceptibility.
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Affiliation(s)
- Lisa J Martin
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio
| | - Hua He
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Margaret H Collins
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Division of Pathology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - J Pablo Abonia
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joceyln M Biagini Myers
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Michael Eby
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hanna Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Leah C Kottyan
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gurjit K Khurana Hershey
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Marc E Rothenberg
- Department of Pediatrics, University of Cincinnati Medical School, Cincinnati, Ohio; Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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Changes in DNA methylation in naïve T helper cells regulate the pathophysiological state in minimal-change nephrotic syndrome. BMC Res Notes 2017; 10:480. [PMID: 28915836 PMCID: PMC5603023 DOI: 10.1186/s13104-017-2719-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 07/29/2017] [Indexed: 11/13/2022] Open
Abstract
Background DNA methylation plays a crucial role in regulating transcription, and changes in DNA methylation affect gene expression and disease development. Minimal change nephrotic syndrome (MCNS) has been reported to involve immunological disturbances. Since the characteristic features of the disease include recurrent relapse and sex and age preference, the disease pathogenesis may be partly related to epigenetic changes. However, little is known about these changes. Methods We analyzed genome-wide DNA methylation using the microarray-based integrated analysis of methylation by isoschizomers method. This method was used to evaluate methylation in monocytes (patient number; n = 6) and naïve T helper cells (n = 4) from the peripheral blood of MCNS patients both in relapse and following remission and that of healthy controls (n = 5). Results In total, 85 co-occurring genes were identified in naïve T helper cells, while 4 such genes were identified in monocytes, which were common among the 3 following comparisons for changes in DNA methylation using sample pairs: (1) relapse versus remission, (2) relapse versus controls, and (3) remission versus controls. In 82 of 85 co-occurring genes (96.5%) in naïve T helper cells, the level of DNA methylation was altered according to disease activity, but was not related to disease activity in the 4 genes detected in monocytes. Conclusions Therefore, in 82 co-occurring genes in naïve T helper cells, the regulation of DNA methylation was well correlated with the clinical and pathophysiological state. Our genome-wide approach to analyze DNA methylation provides further insight into the pathogenesis of MCNS and indicates potential prediction and diagnostic tool for the disease. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2719-1) contains supplementary material, which is available to authorized users.
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Yang IV, Lozupone CA, Schwartz DA. The environment, epigenome, and asthma. J Allergy Clin Immunol 2017; 140:14-23. [PMID: 28673400 DOI: 10.1016/j.jaci.2017.05.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/21/2022]
Abstract
Asthma prevalence has been on the increase, especially in North America compared with other continents. However, the prevalence of asthma differs worldwide, and in many countries the prevalence is stable or decreasing. This highlights the influence of environmental exposures, such as allergens, air pollution, and the environmental microbiome, on disease etiology and pathogenesis. The epigenome might provide the unifying mechanism that translates the influence of environmental exposures to changes in gene expression, respiratory epithelial function, and immune cell skewing that are hallmarks of asthma. In this review we will introduce the concept of the environmental epigenome in asthmatic patients, summarize previous publications of relevance to this field, and discuss future directions.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, Colo.
| | - Catherine A Lozupone
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - David A Schwartz
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Denver, Colo
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Li H, Lu H, Tang W, Zuo J. Targeting methionine cycle as a potential therapeutic strategy for immune disorders. Expert Opin Ther Targets 2017; 21:1-17. [PMID: 28829212 DOI: 10.1080/14728222.2017.1370454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Methionine cycle plays an essential role in regulating many cellular events, especially transmethylation reactions, incorporating the methyl donor S-adenosylmethionine (SAM). The transmethylations and substances involved in the cycle have shown complicated effects and mechanisms on immunocytes developments and activations, and exert crucial impacts on the pathological processes in immune disorders. Areas covered: Methionine cycle has been considered as an effective means of drug developments. This review discussed the role of methionine cycle in immune responses and summarized the potential therapeutic strategies based on the cycle, including SAM analogs, methyltransferase inhibitors, S-adenosylhomocysteine hydrolase (SAHH) inhibitors, adenosine receptors specific agonists or antagonists and homocysteine (Hcy)-lowering reagents, in treating human immunodeficiency virus (HIV) infections, systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), systemic sclerosis (SSc) and other immune disorders. Expert opinion: New targets and biomarkers grown out of methionine cycle have developed rapidly in the past decades. However, impacts of epigenetic regulations on immune disorders are unclear and whether the substances in methionine cycle can be clarified as biomarkers remains controversial. Therefore, further elucidation on the role of epigenetic regulations and substances in methionine cycle may contribute to exploring the cycle-derived biomarkers and drugs in immune disorders.
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Affiliation(s)
- Heng Li
- a Laboratory of Immunopharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
- b College of Pharmacy , University of Chinese Academy of Sciences , Beijing , China
| | - Huimin Lu
- a Laboratory of Immunopharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
- b College of Pharmacy , University of Chinese Academy of Sciences , Beijing , China
| | - Wei Tang
- a Laboratory of Immunopharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
- b College of Pharmacy , University of Chinese Academy of Sciences , Beijing , China
| | - Jianping Zuo
- a Laboratory of Immunopharmacology, State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
- b College of Pharmacy , University of Chinese Academy of Sciences , Beijing , China
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11
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Zhu Y, Qiu Y, Yu H, Yi S, Su W, Kijlstra A, Yang P. Aberrant DNA methylation of GATA binding protein 3 (GATA3), interleukin-4 (IL-4), and transforming growth factor-β (TGF-β) promoters in Behcet's disease. Oncotarget 2017; 8:64263-64272. [PMID: 28969068 PMCID: PMC5610000 DOI: 10.18632/oncotarget.19500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 06/12/2017] [Indexed: 12/18/2022] Open
Abstract
The pathogenesis of Behcet's disease (BD) remains poorly understood. The purpose of this study was to investigate whether an aberrant DNA methylation of transcriptional and inflammatory factors, including TBX21, GATA3, RORγt, FOXP3, IFN-γ, IL-4, IL-17A and TGF-β, in CD4+T confers risk to BD. We found that the promoter methylation level of GATA3, IL-4 and TGF-β was significantly up-regulated in active BD patients and negatively correlated with the corresponding mRNA expression. The mRNA expression of GATA3 and TGF-β was markedly down-regulated in active BD patients compared to healthy individuals. Treatment with corticosteroids and cyclosporine (CsA) resulted in a decrease of the methylation level of GATA3 and TGF-β in inactive BD patients. Our results suggest that an aberrant DNA methylation of GATA3 and TGF-β is associated with their mRNA expression and participates in the pathogenesis of BD.
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Affiliation(s)
- Yunyun Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Yiguo Qiu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Shenglan Yi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Wencheng Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
| | - Aize Kijlstra
- University Eye Clinic Maastricht, Maastricht, The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Chongqing, China
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12
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Wang CM, Chang CB, Chan MW, Wen ZH, Wu SF. Dust mite allergen-specific immunotherapy increases IL4 DNA methylation and induces Der p-specific T cell tolerance in children with allergic asthma. Cell Mol Immunol 2017; 15:963-972. [PMID: 28603280 DOI: 10.1038/cmi.2017.26] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/25/2017] [Accepted: 03/25/2017] [Indexed: 12/23/2022] Open
Abstract
Allergen-specific immunotherapy (allergen-SIT) is a highly effective treatment for children with allergic asthma (AA), an immune-mediated chronic disease leading to bronchial muscle hypertrophy and airway obstruction in response to specific allergens. T helper cells and secreted cytokines play important roles in the pathogenesis of asthma, and epigenetic modulation controls genes important for T cell development and cytokine expression. This study evaluated T helper cell-secreted cytokines and DNA methylation patterns in children treated with Dermatophagoides pteronyssinus (Der p) allergen-SIT. Our results showed that after Der p challenge, peripheral blood mononuclear cells (PBMCs) from the SIT group, compared with the non-SIT AA group, produced lower levels of IL-4, IL-5 and IL-2. The SIT group, compared with the AA group, exhibited decreased sensitivity to the Der p allergen, concurrent with IL-4 down-modulation due to increased promoter DNA methylation, as estimated in PBMCs. Our results showed that SIT decreased IL-4 and IL-5, and inhibited T cell proliferation, by inhibiting IL-2 production after the specific allergen challenge. These results suggest that decreased IL-2 production and increased IL-4 cytokine promoter methylation is a potential mechanism of Der p-specific allergen desensitization immunotherapy.
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Affiliation(s)
- Chuang-Ming Wang
- Department of Pediatrics, Ditmanson Medical Foundation Chia-Yi Christian Hospital, 60002, Chia-Yi, Taiwan, China.,Department of Nursing, Chang Gung University of Science and Technology, 61363, Chia-Yi, Taiwan, China
| | - Chia-Bin Chang
- Department of Life Science and Institute of Molecular Biology, National Chung-Cheng University, 62102, Chia-Yi, Taiwan, China
| | - Michael Wy Chan
- Department of Life Science and Institute of Molecular Biology, National Chung-Cheng University, 62102, Chia-Yi, Taiwan, China
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, Asia-Pacific Ocean Research Center, National Sun Yat-Sen University, 80424, Kaohsiung, Taiwan, China
| | - Shu-Fen Wu
- Department of Life Science and Institute of Molecular Biology, National Chung-Cheng University, 62102, Chia-Yi, Taiwan, China.
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13
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Sardecka I, Krogulska A, Toporowska-Kowalska E. The influence of dietary immunomodulatory factors on development of food allergy in children. Postepy Dermatol Alergol 2017; 34:89-96. [PMID: 28507485 PMCID: PMC5420598 DOI: 10.5114/pdia.2016.63955] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023] Open
Abstract
In the last few years many studies have been conducted on the role of dietary and environmental factors in the prevention of allergic diseases among children. Many studies have shown that the diet of pregnant women and children in their early postnatal life, rich in antioxidants, vitamin D, and fatty acids is beneficial as it reduces the risk of allergy in their future life. Moreover, there are many reports about the main role of gut microbiota and probiotics in the allergy prevention, what can indicate new ways of procedures in allergic diseases.
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Affiliation(s)
- Izabela Sardecka
- Department of Paediatric Allergology, Gastroenterology and Nutrition, 3 Chair of Paediatrics, Medical University of Lodz, Lodz, Poland
| | - Aneta Krogulska
- Department of Paediatry, Allergology and Gastroenterology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Poland
| | - Ewa Toporowska-Kowalska
- Department of Paediatric Allergology, Gastroenterology and Nutrition, 3 Chair of Paediatrics, Medical University of Lodz, Lodz, Poland
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14
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Li JY, Zhang Y, Lin XP, Ruan Y, Wang Y, Wang CS, Zhang L. Association between DNA hypomethylation at IL13 gene and allergic rhinitis in house dust mite-sensitized subjects. Clin Exp Allergy 2016; 46:298-307. [PMID: 26399722 DOI: 10.1111/cea.12647] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 08/28/2015] [Accepted: 09/16/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND Allergic rhinitis (AR) is a complex disease, in which gene-environment interactions contribute to its pathogenesis. Epigenetic modifications such as DNA methylation play an important role in the regulation of gene function. As IL13, a pleiotropic cytokine, may be important in conferring susceptibility to AR, the aim of the present work was to assess the relationship between a CpG island methylation status at the upstream of IL13 gene and house dust mite (HDM)-sensitized AR in Han Chinese subjects. METHODS A total of 60 patients with HDM-sensitized AR and 65 control subjects were enrolled as two independent cohorts from Beijing and Liaoning. MassARRAY EpiTYPER and pyrosequencing was used to systematically screen the status of DNA methylation in peripheral blood leucocytes. IL13 mRNA expression was measured by real-time quantitative PCR. Electrophoretic mobility shift assay was used to assess the function of methylation site. RESULTS The mean level of methylation was decreased in the AR patient group compared with the control group (P = 0.01). Two of a total of 33 IL13CpG units analysed (CpG units 24 : 25 : 26 and 38 : 39) showed significant differences in methylation status between the AR patient group and the control group, with DNA hypomethylation at CpG38 significantly associated with higher risk of HDM-sensitized AR in both independent cohorts and a combined cohort (Beijing: OR = 1.24, 95%CI = 1.01-1.52, P = 0.036; Liaoning: OR = 1.62, 95%CI = 1.11-2.38, P = 0.013; Combined: OR = 1.31, 95%CI = 1.10-1.56, P = 0.002). Methylation level of CpG38 correlated negatively with both IL13 mRNA expression and serum total IgE level and affected the binding affinity of SP1. CONCLUSIONS DNA hypomethylation of IL13 gene may be associated with increased risk of AR from HDM sensitization.
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Affiliation(s)
- J Y Li
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Y Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - X P Lin
- Center of Allergy and Immunotherapy, The General Hospital of Shenyang Military Command, Shenyang, China
| | - Y Ruan
- Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Y Wang
- Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - C S Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
| | - L Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal diseases, Beijing Institute of Otolaryngology, Beijing, China.,Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China
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15
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Wiencke JK, Butler R, Hsuang G, Eliot M, Kim S, Sepulveda MA, Siegel D, Houseman EA, Kelsey KT. The DNA methylation profile of activated human natural killer cells. Epigenetics 2016; 11:363-80. [PMID: 26967308 DOI: 10.1080/15592294.2016.1163454] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Natural killer (NK) cells are now recognized to exhibit characteristics akin to cells of the adaptive immune system. The generation of adaptive memory is linked to epigenetic reprogramming including alterations in DNA methylation. The study herein found reproducible genome wide DNA methylation changes associated with human NK cell activation. Activation led predominately to CpG hypomethylation (81% of significant loci). Bioinformatics analysis confirmed that non-coding and gene-associated differentially methylated sites (DMS) are enriched for immune related functions (i.e., immune cell activation). Known DNA methylation-regulated immune loci were also identified in activated NK cells (e.g., TNFA, LTA, IL13, CSF2). Twenty-one loci were designated high priority and further investigated as potential markers of NK activation. BHLHE40 was identified as a viable candidate for which a droplet digital PCR assay for demethylation was developed. The assay revealed high demethylation in activated NK cells and low demethylation in naïve NK, T- and B-cells. We conclude the NK cell methylome is plastic with potential for remodeling. The differentially methylated region signature of activated NKs revealed similarities with T cell activation, but also provided unique biomarker candidates of NK activation, which could be useful in epigenome-wide association studies to interrogate the role of NK subtypes in global methylation changes associated with exposures and/or disease states.
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Affiliation(s)
- John K Wiencke
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Rondi Butler
- b Brown University , Department of Epidemiology , Providence , RI
| | - George Hsuang
- a Department of Neurological Surgery , University of California San Francisco , San Francisco , CA
| | - Melissa Eliot
- b Brown University , Department of Epidemiology , Providence , RI
| | - Stephanie Kim
- b Brown University , Department of Epidemiology , Providence , RI
| | - Manuel A Sepulveda
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - Derick Siegel
- d Janssen Oncology Therapeutic Area, Janssen Research and Development, LLC, Pharmaceutical Companies of Johnson & Johnson , 1400 Welsh and McKean Roads, Spring House , PA
| | - E Andres Houseman
- e University of Oregon, College of Public Health and Human Science , Corvallis , OR
| | - Karl T Kelsey
- b Brown University , Department of Epidemiology , Providence , RI.,c Department of Laboratory Medicine and Pathology , Providence , RI
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16
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Regulation of IL-4 Expression in Immunity and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 941:31-77. [PMID: 27734408 DOI: 10.1007/978-94-024-0921-5_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IL-4 was first identified as a T cell-derived growth factor for B cells. Studies over the past several decades have markedly expanded our understanding of its cellular sources and function. In addition to T cells, IL-4 is produced by innate lymphocytes, such as NTK cells, and myeloid cells, such as basophils and mast cells. It is a signature cytokine of type 2 immune response but also has a nonimmune function. Its expression is tightly regulated at several levels, including signaling pathways, transcription factors, epigenetic modifications, microRNA, and long noncoding RNA. This chapter will review in detail the molecular mechanism regulating the cell type-specific expression of IL-4 in physiological and pathological type 2 immune responses.
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17
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Yamaguchi T, Takizawa F, Fischer U, Dijkstra JM. Along the Axis between Type 1 and Type 2 Immunity; Principles Conserved in Evolution from Fish to Mammals. BIOLOGY 2015; 4:814-59. [PMID: 26593954 PMCID: PMC4690019 DOI: 10.3390/biology4040814] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/10/2015] [Accepted: 10/19/2015] [Indexed: 02/07/2023]
Abstract
A phenomenon already discovered more than 25 years ago is the possibility of naïve helper T cells to polarize into TH1 or TH2 populations. In a simplified model, these polarizations occur at opposite ends of an "immune 1-2 axis" (i1-i2 axis) of possible conditions. Additional polarizations of helper/regulatory T cells were discovered later, such as for example TH17 and Treg phenotypes; although these polarizations are not selected by the axis-end conditions, they are affected by i1-i2 axis factors, and may retain more potential for change than the relatively stable TH1 and TH2 phenotypes. I1-i2 axis conditions are also relevant for polarizations of other types of leukocytes, such as for example macrophages. Tissue milieus with "type 1 immunity" ("i1") are biased towards cell-mediated cytotoxicity, while the term "type 2 immunity" ("i2") is used for a variety of conditions which have in common that they inhibit type 1 immunity. The immune milieus of some tissues, like the gills in fish and the uterus in pregnant mammals, probably are skewed towards type 2 immunity. An i2-skewed milieu is also created by many tumors, which allows them to escape eradication by type 1 immunity. In this review we compare a number of i1-i2 axis factors between fish and mammals, and conclude that several principles of the i1-i2 axis system seem to be ancient and shared between all classes of jawed vertebrates. Furthermore, the present study is the first to identify a canonical TH2 cytokine locus in a bony fish, namely spotted gar, in the sense that it includes RAD50 and bona fide genes of both IL-4/13 and IL-3/ IL-5/GM-CSF families.
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Affiliation(s)
- Takuya Yamaguchi
- Laboratory of Fish Immunology, Institute of Infectology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany.
| | - Fumio Takizawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Uwe Fischer
- Laboratory of Fish Immunology, Institute of Infectology, Friedrich-Loeffler-Institut, Südufer 10, Greifswald-Insel Riems 17493, Germany.
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Dengakugakubo 1-98, Toyoake, Aichi 470-1192, Japan.
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18
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De Rosa V, Galgani M, Santopaolo M, Colamatteo A, Laccetti R, Matarese G. Nutritional control of immunity: Balancing the metabolic requirements with an appropriate immune function. Semin Immunol 2015; 27:300-9. [PMID: 26527507 DOI: 10.1016/j.smim.2015.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022]
Abstract
The immune system is a highly integrated network of cells sensitive to a number of environmental factors. Interestingly, recent years have seen a dramatic increase in our understanding of how diet makes a crucial contribution to human health, affecting the immune system, secretion of adipocytokines and metabolic pathways. Recent experimental evidence indicates that diet and its components are able to profoundly influence immune responses, thus affecting the development of inflammatory and autoimmune diseases. This review aims to discuss some of the main topics concerning the impact of nutrients and their relative composition on immune cell development and function that may be particularly important for regulating the balance between inflammatory and tolerogenic processes. We also highlight the effects of diet on commensal bacteria and how changes in the composition of the microbiota alter intestinal and systemic immune homeostasis. Finally, we summarize the effects of dietary compounds on epigenetic mechanisms involved in the regulation of several immune related genes.
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Affiliation(s)
- Veronica De Rosa
- Laboratorio di Immunologia, Istituto di Endocrinologia e Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli 80131, Italy; Unità di NeuroImmunologia, Fondazione Santa Lucia, Roma 00143, Italy
| | - Mario Galgani
- Laboratorio di Immunologia, Istituto di Endocrinologia e Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli 80131, Italy
| | - Marianna Santopaolo
- Laboratorio di Immunologia, Istituto di Endocrinologia e Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli 80131, Italy; Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli "Federico II", Napoli 80131, Italy
| | - Alessandra Colamatteo
- Unità di NeuroImmunologia, Fondazione Santa Lucia, Roma 00143, Italy; Dipartimento di Medicina e Chirurgia, Università di Salerno, Baronissi Campus, Baronissi 84081, Salerno, Italy
| | - Roberta Laccetti
- Laboratorio di Immunologia, Istituto di Endocrinologia e Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (IEOS-CNR), Napoli 80131, Italy; Dipartimento di Medicina e Chirurgia, Università di Salerno, Baronissi Campus, Baronissi 84081, Salerno, Italy
| | - Giuseppe Matarese
- Dipartimento di Medicina e Chirurgia, Università di Salerno, Baronissi Campus, Baronissi 84081, Salerno, Italy; IRCCS MultiMedica, Milano 20138, Italy.
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19
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Epigenetic dynamics in immunity and autoimmunity. Int J Biochem Cell Biol 2015; 67:65-74. [DOI: 10.1016/j.biocel.2015.05.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 02/01/2023]
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20
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Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA. DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol 2015; 136:69-80. [PMID: 25769910 DOI: 10.1016/j.jaci.2015.01.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Epigenetic marks are heritable, influenced by the environment, direct the maturation of T lymphocytes, and in mice enhance the development of allergic airway disease. Thus it is important to define epigenetic alterations in asthmatic populations. OBJECTIVE We hypothesize that epigenetic alterations in circulating PBMCs are associated with allergic asthma. METHODS We compared DNA methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy control subjects by using DNA and RNA from PBMCs. Results were validated in an independent population of asthmatic patients. RESULTS Comparing asthmatic patients (n = 97) with control subjects (n = 97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthma, including IL13, RUNX3, and specific genes relevant to T lymphocytes (TIGIT). Among asthmatic patients, 11 differentially methylated regions were associated with higher serum IgE concentrations, and 16 were associated with percent predicted FEV1. Hypomethylated and hypermethylated regions were associated with increased and decreased gene expression, respectively (P < 6 × 10(-12) for asthma and P < .01 for IgE). We further explored the relationship between DNA methylation and gene expression using an integrative analysis and identified additional candidates relevant to asthma (IL4 and ST2). Methylation marks involved in T-cell maturation (RUNX3), TH2 immunity (IL4), and oxidative stress (catalase) were validated in an independent asthmatic cohort of children living in the inner city. CONCLUSIONS Our results demonstrate that DNA methylation marks in specific gene loci are associated with asthma and suggest that epigenetic changes might play a role in establishing the immune phenotype associated with asthma.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - Brent S Pedersen
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Andrew Liu
- Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | - Michelle A Gill
- University of Texas, Southwestern Medical Center, Dallas, Tex
| | | | | | - Corinne E Hennessy
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Elizabeth J Davidson
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colo
| | - Peter Gergen
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
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21
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Komori HK, Hart T, LaMere SA, Chew PV, Salomon DR. Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. THE JOURNAL OF IMMUNOLOGY 2015; 194:1565-79. [PMID: 25576597 DOI: 10.4049/jimmunol.1401162] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Memory T cells are primed for rapid responses to Ag; however, the molecular mechanisms responsible for priming remain incompletely defined. CpG methylation in promoters is an epigenetic modification, which regulates gene transcription. Using targeted bisulfite sequencing, we examined methylation of 2100 genes (56,000 CpGs) mapped by deep sequencing of T cell activation in human naive and memory CD4 T cells. Four hundred sixty-six CpGs (132 genes) displayed differential methylation between naive and memory cells. Twenty-one genes exhibited both differential methylation and gene expression before activation, linking promoter DNA methylation states to gene regulation; 6 of 21 genes encode proteins closely studied in T cells, whereas 15 genes represent novel targets for further study. Eighty-four genes demonstrated differential methylation between memory and naive cells that correlated to differential gene expression following activation, of which 39 exhibited reduced methylation in memory cells coupled with increased gene expression upon activation compared with naive cells. These reveal a class of primed genes more rapidly expressed in memory compared with naive cells and putatively regulated by DNA methylation. These findings define a DNA methylation signature unique to memory CD4 T cells that correlates with activation-induced gene expression.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Traver Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Pamela V Chew
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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22
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Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol 2013; 118:37-128. [PMID: 23683942 DOI: 10.1016/b978-0-12-407708-9.00002-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Epigenetics encompasses transient and heritable modifications to DNA and nucleosomes in the native chromatin context. For example, enzymatic addition of chemical moieties to the N-terminal "tails" of histones, particularly acetylation and methylation of lysine residues in the histone tails of H3 and H4, plays a key role in regulation of gene transcription. The modified histones, which are physically associated with gene regulatory regions that typically occur within conserved noncoding sequences, play a functional role in active, poised, or repressed gene transcription. The "histone code" defined by these modifications, along with the chromatin-binding acetylases, deacetylases, methylases, demethylases, and other enzymes that direct modifications resulting in specific patterns of histone modification, shows considerable evolutionary conservation from yeast to humans. Direct modifications at the DNA level, such as cytosine methylation at CpG motifs that represses promoter activity, are another highly conserved epigenetic mechanism of gene regulation. Furthermore, epigenetic modifications at the nucleosome or DNA level can also be coupled with higher-order intra- or interchromosomal interactions that influence the location of regulatory elements and that can place them in an environment of specific nucleoprotein complexes associated with transcription. In the mammalian immune system, epigenetic gene regulation is a crucial mechanism for a range of physiological processes, including the innate host immune response to pathogens and T cell differentiation driven by specific patterns of cytokine gene expression. Here, we will review current findings regarding epigenetic regulation of cytokine genes important in innate and/or adaptive immune responses, with a special focus upon the tumor necrosis factor/lymphotoxin locus and cytokine-driven CD4+ T cell differentiation into the Th1, Th2, and Th17 lineages.
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23
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Michel S, Busato F, Genuneit J, Pekkanen J, Dalphin JC, Riedler J, Mazaleyrat N, Weber J, Karvonen AM, Hirvonen MR, Braun-Fahrländer C, Lauener R, von Mutius E, Kabesch M, Tost J. Farm exposure and time trends in early childhood may influence DNA methylation in genes related to asthma and allergy. Allergy 2013; 68:355-64. [PMID: 23346934 DOI: 10.1111/all.12097] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2012] [Indexed: 01/17/2023]
Abstract
BACKGROUND Genetic susceptibility and environmental influences are important contributors to the development of asthma and atopic diseases. Epigenetic mechanisms may facilitate gene by environment interactions in these diseases. METHODS We studied the rural birth cohort PASTURE (Protection against allergy: study in rural environments) to investigate (a) whether epigenetic patterns in asthma candidate genes are influenced by farm exposure in general, (b) change over the first years of life, and (c) whether these changes may contribute to the development of asthma. DNA was extracted from cord blood and whole blood collected at the age of 4.5 years in 46 samples per time point. DNA methylation in 23 regions in ten candidate genes (ORMDL1, ORMDL2, ORMDL3, CHI3L1, RAD50, IL13, IL4, STAT6, FOXP3, and RUNX3) was assessed by pyrosequencing, and differences between strata were analyzed by nonparametric Wilcoxon-Mann-Whitney tests. RESULTS In cord blood, regions in ORMDL1 and STAT6 were hypomethylated in DNA from farmers' as compared to nonfarmers' children, while regions in RAD50 and IL13 were hypermethylated (lowest P-value (STAT6) = 0.001). Changes in methylation over time occurred in 15 gene regions (lowest P-value (IL13) = 1.57*10(-8)). Interestingly, these differences clustered in the genes highly associated with asthma (ORMDL family) and IgE regulation (RAD50, IL13, and IL4), but not in the T-regulatory genes (FOXP3, RUNX3). CONCLUSIONS In this first pilot study, DNA methylation patterns change significantly in early childhood in specific asthma- and allergy-related genes in peripheral blood cells, and early exposure to farm environment seems to influence methylation patterns in distinct genes.
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Affiliation(s)
| | - F. Busato
- Laboratory for Epigenetics; Centre National de Génotypage; CEA-Institut de Génomique; Evry; France
| | - J. Genuneit
- Ulm University; Institute of Epidemiology and Medical Biometry; Ulm; Germany
| | | | - J.-C. Dalphin
- Department of Respiratory Disease; Université de Franche-Comté; University Hospital; Besancon; France
| | - J. Riedler
- Children's Hospital Schwarzach; Schwarzach; Austria
| | - N. Mazaleyrat
- Laboratory for Epigenetics; Centre National de Génotypage; CEA-Institut de Génomique; Evry; France
| | - J. Weber
- LMU Munich; University Children's Hospital; Munich; Germany
| | - A. M. Karvonen
- Department of Environmental Health; National Institute for Health and Welfare; Kuopio; Finland
| | | | | | | | - E. von Mutius
- LMU Munich; University Children's Hospital; Munich; Germany
| | | | - J. Tost
- Laboratory for Epigenetics; Centre National de Génotypage; CEA-Institut de Génomique; Evry; France
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Transcription factor YY1 is essential for regulation of the Th2 cytokine locus and for Th2 cell differentiation. Proc Natl Acad Sci U S A 2012; 110:276-81. [PMID: 23248301 DOI: 10.1073/pnas.1214682110] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Th2 locus control region (LCR) has been shown to be important in efficient and coordinated cytokine gene regulation during Th2 cell differentiation. However, the molecular mechanism for this is poorly understood. To study the molecular mechanism of the Th2 LCR, we searched for proteins binding to it. We discovered that transcription factor YY1 bound to the LCR and the entire Th2 cytokine locus in a Th2-specific manner. Retroviral overexpression of YY1 induced Th2 cytokine expression. CD4-specific knockdown of YY1 in mice caused marked reduction in Th2 cytokine expression, repressed chromatin remodeling, decreased intrachromosomal interactions, and resistance in an animal model of asthma. YY1 physically associated with GATA-binding protein-3 (GATA3) and is required for GATA3 binding to the locus. YY1 bound to the regulatory elements in the locus before GATA3 binding. Thus, YY1 cooperates with GATA3 and is required for regulation of the Th2 cytokine locus and Th2 cell differentiation.
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Abstract
Although substantial progress has been made in understanding the clinical, radiological, and pathological manifestations of fibrosing interstitial lung diseases (ILD), it remains difficult for the clinician to predict the clinical course or the response to therapy for the subtypes of ILD, even from individual to individual with the same diagnosis. This article reviews the genetic and environmental causes of pulmonary fibrosis, specifically focusing on genetic and epigenetic variants of MUC5B and several types of ILD, to discuss why only some individuals with the MUC5B promoter polymorphism develop pulmonary fibrosis. Once we discover how these genetic and epigenetic risks lead to the development of ILD, we and others can apply these discoveries to: (1) identify individuals at risk of developing ILD, (2) diagnose the condition at an earlier stage, (3) identify novel mechanisms that cause ILD, and (4) eventually develop personalized therapeutic strategies for intervention.
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Yang IV, Schwartz DA. Epigenetic mechanisms and the development of asthma. J Allergy Clin Immunol 2012; 130:1243-55. [PMID: 23026498 PMCID: PMC3518374 DOI: 10.1016/j.jaci.2012.07.052] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 12/19/2022]
Abstract
Asthma is heritable, influenced by the environment, and modified by in utero exposures and aging; all of these features are also common to epigenetic regulation. Furthermore, the transcription factors that are involved in the development of mature T cells that are critical to the T(H)2 immune phenotype in asthmatic patients are regulated by epigenetic mechanisms. Epigenetic marks (DNA methylation, modifications of histone tails, and noncoding RNAs) work in concert with other components of the cellular regulatory machinery to control the spatial and temporal levels of expressed genes. Technology to measure epigenetic marks on a genomic scale and comprehensive approaches to data analysis have recently emerged and continue to improve. Alterations in epigenetic marks have been associated with exposures relevant to asthma, particularly air pollution and tobacco smoke, as well as asthma phenotypes, in a few population-based studies. On the other hand, animal studies have begun to decipher the role of epigenetic regulation of gene expression associated with the development of allergic airway disease. Epigenetic mechanisms represent a promising line of inquiry that might, in part, explain the inheritance and immunobiology of asthma.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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27
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Jacoby M, Gohrbandt S, Clausse V, Brons NH, Muller CP. Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics 2012; 7:1421-34. [PMID: 23151460 DOI: 10.4161/epi.22845] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation regulates gene expression in a cell-type specific way. Although peripheral blood mononuclear cells (PBMCs) comprise a heterogeneous cell population, most studies of DNA methylation in blood are performed on total mononuclear cells. In this study, we investigated high resolution methylation profiles of 58 CpG sites dispersed over eight immune response genes in multiple purified blood cells from healthy adults and newborns. Adjacent CpG sites showed methylation levels that were increasingly correlated in adult blood vs. cord blood. Thus, while interindividual variability increases from newborn to adult blood, the underlying methylation changes may not be merely stochastic, but seem to be orchestrated as clusters of adjacent CpG sites. Multiple linear regression analysis showed that interindividual methylation variability was influenced by distance of average methylation levels to the closest border (0 or 100%), presence of transcription factor binding sites, CpG conservation across species and age. Furthermore, CD4+ and CD14+ cell types were negative predictors of methylation variability. Concerns that PBMC methylation differences may be confounded by variations in blood cell composition were justified for CpG sites with large methylation differences across cell types, such as in the IFN-γ gene promoter. Taken together, our data suggest that unsorted mononuclear cells are reasonable surrogates of CD8+ and, to a lesser extent, CD4+ T cell methylation in adult peripheral, but not in neonatal, cord blood.
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Affiliation(s)
- Monique Jacoby
- Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, Luxembourg, Luxembourg
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28
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Suarez-Alvarez B, Rodriguez RM, Fraga MF, López-Larrea C. DNA methylation: a promising landscape for immune system-related diseases. Trends Genet 2012; 28:506-14. [PMID: 22824525 DOI: 10.1016/j.tig.2012.06.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/13/2012] [Accepted: 06/20/2012] [Indexed: 01/31/2023]
Abstract
During hematopoiesis, a unique hematopoietic stem cell (HSC) from the bone marrow gives rise to a subset of mature blood cells that directs all the immune responses. Recent studies have shown that this well-defined, hierarchical process is regulated in part by epigenetic mechanisms. Changes in the DNA methylation profile have a critical role in the division of these stem cells into the myeloid and lymphoid lineages and in the establishment of a specific phenotype and functionality in each terminally differentiated cell type. In this review, we describe how the DNA methylation patterns are modified during hematopoietic differentiation and what their role is in cell plasticity and immune function. An in-depth knowledge of these epigenetic mechanisms will help clarify how cell type-specific gene programs are established, and how they can be leveraged in the development of novel strategies for treating immune system-related pathologies.
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DNA methylation changes between relapse and remission of minimal change nephrotic syndrome. Pediatr Nephrol 2012; 27:2233-41. [PMID: 22855301 PMCID: PMC3491205 DOI: 10.1007/s00467-012-2248-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 05/31/2012] [Accepted: 06/11/2012] [Indexed: 01/29/2023]
Abstract
BACKGROUND DNA methylation of gene promoters is associated with transcriptional inactivation. Changes in DNA methylation can lead to differences in gene expression levels and thereby influence disease development. We hypothesized that epigenetics underlies the pathogenesis of minimal change nephrotic syndrome (MCNS). METHODS Genome-wide DNA methylation changes between relapse and remission in monocytes (n = 6) and naive T helper cells (Th0s) (n = 4) isolated from patients with MCNS were investigated using the microarray-based integrated analysis of methylation by isochizomers (MIAMI) method. We confirmed the MIAMI results using bisulfite-pyrosequencing analysis. Expression analysis was performed using quantitative real-time PCR. RESULTS Three gene loci (GATA2, PBX4, and NYX) were significantly less methylated in Th0s during relapse than in remission, compared to none in monocytes. In addition, the distance distribution from the regression line of all probes in MIAMI was significantly different between monocytes and Th0s. The mRNA levels of the three genes in Th0s were not significantly different between relapse and remission. CONCLUSIONS Our results demonstrate that the change in DNA methylation patterns from remission to relapse in MCNS occurs predominantly in Th0s rather than in monocytes and suggest that epigenetic regulation in Th0s underlies the pathogenesis of MCNS.
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Richardson B, Sawalha AH, Ray D, Yung R. Murine models of lupus induced by hypomethylated T cells (DNA hypomethylation and lupus…). Methods Mol Biol 2012; 900:169-80. [PMID: 22933069 DOI: 10.1007/978-1-60761-720-4_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
CD4+ T cell DNA hypomethylation may contribute to the development of drug induced and idiopathic human lupus. Inhibiting DNA methylation in mature CD4+ T cells causes MHC-specific autoreactivity in vitro. The lupus-inducing drugs hydralazine and procainamide also inhibit T cell DNA methylation and induce autoreactivity, and T cells from patients with active lupus have hypomethylated DNA and a similarly autoreactive T cell subset. Further, T cells treated with DNA methylation inhibitors demethylate the same sequences that demethylate in T cells from patients with active lupus. The pathologic significance of the autoreactivity induced by inhibiting T cell DNA methylation has been tested by treating murine T cells in vitro with drugs which modify DNA methylation, then injecting the cells into syngeneic female mice. Mice receiving CD4+ T cells demethylated by a variety of agents including procainamide and hydralazine develop a lupus-like disease. Further, transgenic mice with an inducible T cell DNA methylation defect also develop lupus-like autoimmunity. This chapter describes the protocols for inducing autoreactivity in murine T cells in vitro and for inducing autoimmunity in vivo using an adoptive transfer approach or transgenic animal models.
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Affiliation(s)
- Bruce Richardson
- University of Michigan and the Ann Arbor Veteran's Affairs Hospital, Ann Arbor, MI, USA.
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31
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Application of ChIP-Seq and related techniques to the study of immune function. Immunity 2011; 34:830-42. [PMID: 21703538 DOI: 10.1016/j.immuni.2011.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Indexed: 01/02/2023]
Abstract
Behaviors observed at the cellular level such as development and acquisition of effector functions by immune cells result from transcriptional changes. The biochemical mediators of transcription are sequence-specific transcription factors (TFs), chromatin modifying enzymes, and chromatin, the complex of DNA and histone proteins. Covalent modification of DNA and histones, also termed epigenetic modification, influences the accessibility of target sequences for transcription factors on chromatin and the expression of linked genes required for immune functions. Genome-wide techniques such as ChIP-Seq have described the entire "cistrome" of transcription factors involved in specific developmental steps of B and T cells and started to define specific immune responses in terms of the binding profiles of critical effectors and epigenetic modification patterns. Current data suggest that both promoters and enhancers are prepared for action at different stages of activation by epigenetic modification through distinct transcription factors in different cells.
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32
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Yang IV, Schwartz DA. Epigenetic control of gene expression in the lung. Am J Respir Crit Care Med 2011; 183:1295-301. [PMID: 21596832 DOI: 10.1164/rccm.201010-1579pp] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is traditionally defined as the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. There are three main classes of epigenetic marks--DNA methylation, modifications of histone tails, and noncoding RNAs--each of which may be influenced by the environment, diet, diseases, and ageing. Importantly, epigenetic marks have been shown to influence immune cell maturation and are associated with the risk of developing various forms of cancer, including lung cancer. Moreover, there is emerging evidence that these epigenetic marks affect gene expression in the lung and are associated with benign lung diseases, such as asthma, chronic obstructive pulmonary disease, and interstitial lung disease. Technological advances have made it feasible to study epigenetic marks in the lung, and it is anticipated that this knowledge will enhance our understanding of the dynamic biology in the lung and lead to the development of novel diagnostic and therapeutic approaches for our patients with lung disease.
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Affiliation(s)
- Ivana V Yang
- Center for Genes, Environment, and Health, National Jewish Health,Denver, CO 80206, USA.
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33
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Deaton AM, Webb S, Kerr AR, Illingworth RS, Guy J, Andrews R, Bird A. Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res 2011; 21:1074-86. [PMID: 21628449 PMCID: PMC3129250 DOI: 10.1101/gr.118703.110] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 04/15/2011] [Indexed: 12/26/2022]
Abstract
Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, ∼50% of all CGIs are remote from annotated promoters but, nevertheless, often have promoter-like features. To determine the role of CGI methylation in cell differentiation, we analyzed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. Using a method that potentially detects ∼33% of genomic CpGs in the methylated state, we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes. There were, however, many DNA methylation differences between hematopoietic cells and a distantly related tissue, brain. Altered DNA methylation in the immune system occurred predominantly at CGIs within gene bodies, which have the properties of cell type-restricted promoters, but infrequently at annotated gene promoters or CGI flanking sequences (CGI "shores"). Unexpectedly, elevated intragenic CGI methylation correlated with silencing of the associated gene. Differentially methylated intragenic CGIs tended to lack H3K4me3 and associate with a transcriptionally repressive environment regardless of methylation state. Our results indicate that DNA methylation changes play a relatively minor role in the late stages of differentiation and suggest that intragenic CGIs represent regulatory sites of differential gene expression during the early stages of lineage specification.
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Affiliation(s)
- Aimée M. Deaton
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Alastair R.W. Kerr
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Robert S. Illingworth
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Jacky Guy
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Robert Andrews
- Wellcome Trust Sanger Centre, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Adrian Bird
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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Hirasaki Y, Iwamura C, Yamashita M, Ito T, Kitajima M, Shinoda K, Namiki T, Terasawa K, Nakayama T. Repressor of GATA negatively regulates murine contact hypersensitivity through the inhibition of type-2 allergic responses. Clin Immunol 2011; 139:267-76. [PMID: 21398189 DOI: 10.1016/j.clim.2011.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/18/2011] [Accepted: 02/01/2011] [Indexed: 11/29/2022]
Abstract
Repressor of GATA (ROG) inhibits Th2 cell differentiation and allergic airway inflammation in the lung. To determine the role of ROG in the pathogenesis of contact hypersensitivity (CHS), a hapten-induced mouse model of CHS using ROG Tg and ROG-deficient (ROG(-/-)) was used. ROG Tg mice showed little ear swelling, while ROG(-/-) mice showed enhanced ear swelling in comparison to wild type mice. Interstitial edema and mast cell degranulation at the local inflammation sites were mild in ROG Tg mice and exacerbated in ROG(-/-) mice. In addition, the serum total IgE and hapten-specific IgG1 levels were increased in ROG(-/-) mice. Adoptive transfer of ROG(-/-) CD4(+) T cells exacerbated CHS in wild type mice, while transfer of ROG Tg CD4(+) T cells resulted in the attenuation of CHS. These results indicate ROG negatively regulates the induction of CHS by controlling the CD4(+) T cell-mediated allergic responses, including IgE generation and mast cell degranulation.
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Affiliation(s)
- Yoshiro Hirasaki
- Department of Immunology, Graduate School of Medicine, Chiba University, Inohana, Chuo-ku, Chiba, Japan
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35
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Janson PCJ, Linton LB, Ahlén Bergman E, Marits P, Eberhardson M, Piehl F, Malmström V, Winqvist O. Profiling of CD4+ T Cells with Epigenetic Immune Lineage Analysis. THE JOURNAL OF IMMUNOLOGY 2010; 186:92-102. [DOI: 10.4049/jimmunol.1000960] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
Several lines of evidence suggest the involvement of disturbance in epigenetic processes in autoimmune disease. Most noteworthy is the global DNA hypomethylation seen in lupus. Epigenetic states in difference from genetic lesions are potentially reversible and hence candidates for pharmacological intervention. Potential targets for drug development are histone modification and DNA methylating and demethylating enzymes. The most advanced set of drugs in clinical development are histone deacetylase (HDAC) inhibitors. However, the prevalence of DNA hypomethylation in lupus suggests that we should shift our attention from HDAC inhibitors to DNA demethylation inhibitors. MBD2 was recently proposed to be involved in demethylation in T cells in lupus and is, therefore, a candidate target. Although this field is at its infancy, it carries great promise.
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Affiliation(s)
- Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, 3655 Sir William Osler Promenade, Montreal, QC, H3G 1Y6, Canada.
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37
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Epigenetics and chemical safety assessment. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2010; 705:83-95. [DOI: 10.1016/j.mrrev.2010.04.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 03/29/2010] [Accepted: 04/08/2010] [Indexed: 01/01/2023]
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38
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Abstract
Events and exposures in pregnancy can have critical effects on fetal development with lasting implications for subsequent health and disease susceptibility. There is growing interest in how modern environmental changes influence fetal immune development and contribute to the recent epidemic of allergy and other immune disorders. Rising rates of allergic disease in early infancy, together with pre-symptomatic differences in immune function at birth, suggest that antenatal events play a predisposing role in the development of disease. A number of environmental exposures in pregnancy can modify neonatal immune function including diet, microbial exposure and maternal smoking, and there is emerging evidence from animal models that these factors may have epigenetic effects on immune gene expression and disease susceptibility. Furthermore, functional genetic polymorphisms also alter individual vulnerability to the effects of these environmental exposures, highlighting the complexity of gene-environmental interactions in this period. All these observations underscore the need for ongoing research to understand the pathogenesis and rising incidence of disease in the hope of better strategies to reverse this.
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Williams M, Georas S. Gene expression patterns and susceptibility to allergic responses. Expert Rev Clin Immunol 2010; 2:59-73. [PMID: 20477088 DOI: 10.1586/14787210.2.1.59] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Allergic diseases are due to hypersensitive immune responses against otherwise innocuous allergens, and involve the dysregulated expression of numerous genes in cells from both the innate and adaptive immune systems. Allergic diseases are characterized by the enhanced production of type 2 T helper (Th2) cytokines, including interleukin-4, -5 and -13. These cytokines induce many of the pathophysiologic hallmarks of allergy, and their expression is tightly regulated at the level of gene transcription by both positively and negatively-acting transcription factors. In this review, the authors summarize data indicating that some of these factors represent checkpoints in the development of allergic diseases. Th2 gene expression is also controlled at the level of chromatin remodeling, and the implications of chromatin-based Th2 gene regulation in allergic disorders is also discussed. The differentiation of Th2 cells from naive precursors is critically dependent upon instruction received from dendritic cells, although the precise signals involved in this process are not well understood. Current thinking regarding some of the environmental cues interpreted by dendritic cells during allergen encounter, and how they promote Th2 responses will be reviewed. Understanding the cross-talk between dendritic cells and T cells holds great promise for deciphering the dysregulated immune response in allergy.
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Affiliation(s)
- Marc Williams
- Johns Hopkins Asthma & Allergy Center, 5501 Hopkins Bayview CircleBaltimore, MD 21224, USA.
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40
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Hypomethylation of IL10 and IL13 promoters in CD4+ T cells of patients with systemic lupus erythematosus. J Biomed Biotechnol 2010; 2010:931018. [PMID: 20589076 PMCID: PMC2879555 DOI: 10.1155/2010/931018] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 03/23/2010] [Indexed: 11/17/2022] Open
Abstract
Interleukin- (IL-)10 and IL-13 play important roles in Th2 cell differentiation and production of autoantibodies in patients with (SLE). However, the mechanisms leading to IL10 and IL13 overexpression in SLE patients are not well understood. In this study, we confirm that the levels of both IL10 and IL13 mRNA in CD4+ T cells and of serum IL10 and IL13 proteins are increased in SLE patients. We show that the DNA methylation levels within IL10 and IL13 gene regulatory domains are reduced in SLE CD4+ T cells relative to healthy controls and negatively correlate with IL10 and IL13 mRNA expression. Moreover, treating healthy CD4+ T cells with the demethylating agent 5-azacytidine (5-azaC) increased IL10 and IL13 mRNA transcription. Together, our results show that promoter methylation is a determinant of IL10 and IL13 expression in CD4+ T cells, and we propose that DNA hypomethylation leads to IL10 and IL13 overexpression in SLE patients.
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Kiesler P, Haynes PA, Shi L, Kao PN, Wysocki VH, Vercelli D. NF45 and NF90 regulate HS4-dependent interleukin-13 transcription in T cells. J Biol Chem 2010; 285:8256-67. [PMID: 20051514 PMCID: PMC2832977 DOI: 10.1074/jbc.m109.041004] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 12/10/2009] [Indexed: 01/13/2023] Open
Abstract
Expression of the cytokine interleukin-13 (IL13) is critical for Th2 immune responses and Th2-mediated allergic diseases. Activation of human IL13 expression involves chromatin remodeling and formation of multiple DNase I-hypersensitive sites throughout the locus. Among these, HS4 is detected in the distal IL13 promoter in both naive and polarized CD4(+) T cells. We show herein that HS4 acts as a position-independent, orientation-dependent positive regulator of IL13 proximal promoter activity in transiently transfected, activated human CD4(+) Jurkat T cells and primary murine Th2 cells. The 3'-half of HS4 (HS4-3') was responsible for IL13 up-regulation and bound nuclear factor (NF) 90 and NF45, as demonstrated by DNA affinity chromatography coupled with tandem mass spectrometry, chromatin immunoprecipitation, and gel shift analysis. Notably, the CTGTT NF45/NF90-binding motif within HS4-3' was critical for HS4-dependent up-regulation of IL13 expression. Moreover, transfection of HS4-IL13 reporter vectors into primary, in vitro differentiated Th2 cells from wild-type, NF45(+/-), or NF90(+/-) mice showed that HS4 activity was exquisitely dependent on the levels of endogenous NF45 (and to a lesser degree NF90), because HS4-dependent IL13 expression was virtually abrogated in NF45(+/-) cells and reduced in NF90(+/-) cells. Collectively, our results identify NF45 and NF90 as novel regulators of HS4-dependent human IL13 transcription in response to T cell activation.
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Affiliation(s)
- Patricia Kiesler
- From the Functional Genomics Laboratory, Arizona Respiratory Center
| | | | - Lingfang Shi
- the Department of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, California 94305
| | - Peter N. Kao
- the Department of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, California 94305
| | | | - Donata Vercelli
- From the Functional Genomics Laboratory, Arizona Respiratory Center
- Cell Biology
- Arizona Center for the Biology of Complex Diseases, and
- The Bio5 Institute, University of Arizona, Tucson, Arizona 85719 and
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Cuddapah S, Barski A, Zhao K. Epigenomics of T cell activation, differentiation, and memory. Curr Opin Immunol 2010; 22:341-7. [PMID: 20226645 DOI: 10.1016/j.coi.2010.02.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 02/04/2010] [Accepted: 02/11/2010] [Indexed: 11/15/2022]
Abstract
Activation of T cells is an essential step in the immunological response to infection. Although activation of naïve T cells results in proliferation and slow differentiation into cytokine-producing effector cells, antigen engagement with memory cells leads to cytokine production immediately. Even though the cell surface signaling events are similar in both the cases, the outcome is different, suggesting that distinct regulatory mechanisms may exist downstream of the activation signals. Recent advances in the understanding of global epigenetic patterns in T cells have resulted in the appreciation of the role of epigenetic mechanisms in processes such as activation and differentiation. In this review we discuss recent data suggesting that naïve T cell activation, differentiation, and lineage commitment result in epigenetic changes and a fine balance between different histone modifications is required. On the other hand, memory T cells are poised and do not require epigenetic changes for short-term activation.
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Affiliation(s)
- Suresh Cuddapah
- Laboratory of Molecular Immunology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Ferreira MAR, Oates NA, van Vliet J, Zhao ZZ, Ehrich M, Martin NG, Montgomery GW, Whitelaw E, Duffy DL. Characterization of the methylation patterns of MS4A2 in atopic cases and controls. Allergy 2010; 65:333-7. [PMID: 19796196 DOI: 10.1111/j.1398-9995.2009.02135.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND It is largely unknown whether epigenetic modifications of key genes may contribute to the reported maternal effects in atopy. The aim of this study was to characterize the methylation patterns of the membrane-spanning 4-domains, subfamily A, member 2 gene (MS4A2) (beta-chain of the IgE high-affinity receptor), a key gene in the allergic cascade. METHODS Mass spectrometry and bisulphite sequencing were used to measure the methylation of two potential substrates for epigenetic regulation of MS4A2, namely a predicted promoter and a CpG-rich AluSp repeat. Methylation was measured in DNA extracted from peripheral blood lymphocytes of 38 atopic cases and 37 controls. Cases were positive for atopy, asthma, bronchial hyper-responsiveness and had high IgE levels. Both parents of eight atopic cases were also tested. RESULTS The AluSp element was highly methylated across all individuals (mean 0.92, range 0.87-0.94), a pattern inconsistent with classical imprinting. Variation in methylation at this locus was not associated with age, sex, daily steroid use or atopic status, and there were no differences in methylation between mothers and fathers of atopic cases. Bisulphite sequencing analysis of the promoter region showed that it was also not imprinted, and there was no evidence for allele-specific methylation, but we were unable to test for association with atopy status. CONCLUSIONS Methylation levels at the AluSp repeat analysed in MS4A2 were inconsistent with classical imprinting mechanisms and did not associate with atopy status. The promoter region was less methylated but further analysis of this region in larger cohorts is warranted to investigate its role in allergic disease.
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Affiliation(s)
- M A R Ferreira
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Qld, Australia
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Martino DJ, Prescott SL. Silent mysteries: epigenetic paradigms could hold the key to conquering the epidemic of allergy and immune disease. Allergy 2010; 65:7-15. [PMID: 19796189 DOI: 10.1111/j.1398-9995.2009.02186.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Epigenetic mechanisms provide new insights into how environmental changes may mediate the increasing propensity for complex immune diseases such as allergic disease. There is now strong evidence that early environmental exposures play a key role in activating or silencing genes by altering DNA and histone methylation, histone acetylation and chromatin structure. These modifications determine the degree of DNA compaction and accessibility for gene transcription, altering gene expression, phenotype and disease susceptibility. While there is already evidence that a number of early environmental exposures are associated with an increased risk of allergic disease, several new studies indicate in utero microbial and dietary exposures can modify gene expression and allergic disease propensity through epigenetic modification. This review explores the evidence that immune development is under clear epigenetic regulation, including the pattern of T helper (Th)1 and Th2 cell differentiation, regulatory T cell differentiation, and more recently, Th17 development. It also considers the mechanisms of epigenetic regulation and early immune defects in allergy prone neonates. The inherent plasticity conferred by epigenetic mechanisms clearly also provides opportunities for environmental strategies that can re-programme gene expression for disease prevention. Identifying genes that are differentially silenced or activated in relation to subsequent disease will not only assist in identifying causal pathways, but may also help identify the contributing environmental factors.
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Affiliation(s)
- D J Martino
- School of Pediatrics and Child Health Research, University of Western Australia, Perth, Western Australia, Australia
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Cao Y, Vo T, Millien G, Tagne JB, Kotton D, Mason RJ, Williams MC, Ramirez MI. Epigenetic mechanisms modulate thyroid transcription factor 1-mediated transcription of the surfactant protein B gene. J Biol Chem 2009; 285:2152-64. [PMID: 19906647 DOI: 10.1074/jbc.m109.039172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Epigenetic regulation of transcription plays an important role in cell-specific gene expression by altering chromatin structure and access of transcriptional regulators to DNA binding sites. Surfactant protein B (Sftpb) is a developmentally regulated lung epithelial gene critical for lung function. Thyroid transcription factor 1 (Nkx2-1) regulates Sftpb gene expression in various species. We show that Nkx2-1 binds to the mouse Sftpb (mSftpb) promoter in the lung. In a mouse lung epithelial cell line (MLE-15), Nkx2-1 knockdown reduces Sftpb expression, and mutation of Nkx2-1 cis-elements significantly reduces mSftpb promoter activity. Whether chromatin structure modulates Nkx2-1 regulation of Sftpb transcription is unknown. We found that DNA methylation of the mSftpb promoter inversely correlates with known patterns of Sftpb expression in vivo. The mSftpb promoter activity can be manipulated by altering its cytosine methylation status in vitro. Nkx2-1 activation of the mSftpb promoter is impaired by DNA methylation. The unmethylated Sftpb promoter shows an active chromatin structure enriched in the histone modification H3K4me3 (histone 3-lysine 4 trimethylated). The ATP-dependent chromatin remodeling protein Brg1 is recruited to the Sftpb promoter in Sftpb-expressing, but not in non-expressing tissues and cell lines. Brg1 knockdown in MLE-15 cells greatly decreases H3K4me3 levels at the Sftpb promoter region and expression of the Sftpb gene. Brg1 can be co-immunoprecipitated with Nkx2-1 protein. Last, Nkx2-1 and Brg1 with intact ATPase activity are required for mSftpb promoter activation in vitro. Our findings suggest that DNA methylation and chromatin modifications cooperate with Nkx2-1 to regulate Sftpb gene cell specific expression.
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Affiliation(s)
- Yuxia Cao
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA.
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MacFarlane AJ, Strom A, Scott FW. Epigenetics: deciphering how environmental factors may modify autoimmune type 1 diabetes. Mamm Genome 2009; 20:624-32. [PMID: 19697079 DOI: 10.1007/s00335-009-9213-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 07/20/2009] [Indexed: 02/08/2023]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that has increased two- to threefold over the past half century by as yet unknown means. It is generally accepted that T1D is the result of gene-environment interactions, but such rapid increases in incidence are not explained by Mendelian inheritance. There have been numerous advances in our knowledge of the pathogenesis of T1D. Indeed, there has been a large number of genes identified that contribute to risk for this disease and several environmental factors have been proposed. The complexity of such interactions is yet to be understood for any major chronic disease. Epigenetic regulation is one way to explain the rapid increase in incidence and could be a central mechanism by which environmental factors influence development of diabetes. However, there is remarkably little known about the contribution of epigenetics to T1D pathogenesis. Here we speculate on various candidate processes and molecules of the immune and endocrine systems that could modify risk for T1D through epigenetic regulation.
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Affiliation(s)
- Amanda J MacFarlane
- Nutrition Research Division, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A0K9, Canada.
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Santangelo S, Cousins DJ, Winkelmann N, Triantaphyllopoulos K, Staynov DZ. Chromatin structure and DNA methylation of the IL-4 gene in human T(H)2 cells. Chromosome Res 2009; 17:485-96. [PMID: 19521787 DOI: 10.1007/s10577-009-9040-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 04/19/2009] [Accepted: 04/19/2009] [Indexed: 11/25/2022]
Abstract
Human T(H)2 cell differentiation results in the selective demethylation of several specific CpG dinucleotides in the IL-4 and IL-13 genes, which are expressed in activated T(H)2, but not T(H)1, cells. This demethylation is accompanied by the appearance of six DNase I hypersensitive sites within 1.4 kb at the 5'-end of the IL-4 gene. Micrococcal nuclease (MNase) digestion revealed that in both T(H)1 and T(H)2 cells nine nucleosomes with a repeat length of 201 bp are identically positioned around the 5'-end of the IL-4 gene. However, only in T(H)2 cells are six out of the eight intervening linkers exposed to DNase I. This suggests that a major perturbation of the higher-order chromatin structure occurs above the level of the nucleosome in vivo. It is observed in cells that are poised for expression but which are not actively expressing the gene (i.e. resting T(H)2 cells). Notably, all the demethylated CpGs in T(H)2 cells are found in DNA that is accessible to DNase I. This may suggest that the opening of the chromatin structure allows binding of specific trans-acting factors that prevent de novo methylation.
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Ito T, Ito N, Hashizume H, Takigawa M. Roxithromycin inhibits chemokine-induced chemotaxis of Th1 and Th2 cells but regulatory T cells. J Dermatol Sci 2009; 54:185-91. [PMID: 19251402 DOI: 10.1016/j.jdermsci.2009.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 01/23/2009] [Accepted: 01/29/2009] [Indexed: 10/21/2022]
Abstract
BACKGROUND Roxithromycin (RXM), a 14-member macrolide antibiotic, has a variety of bioregulatory functions such as anti-inflammatory effects, anti-oxidant effects, and modulation of immune responses. OBJECTIVES In this study, we analyzed the effect of RXM on chemokine-induced chemotaxis of Th1, Th2, and regulatory T (Treg) cells established from three normal human peripheral blood lymphocytes by the reported methods. METHODS AND RESULTS Incubation with 10 microM RXM for 18 h did not alter the expression profile of CXCR3 on Th1 cells and CCR4 on Th2 and Treg cells. However, upon RXM preincubation, the migration of Th1 cells to IP-10 and Th2 cells to TARC was partially suppressed, although RXM did not influence Treg cell migration. Erythromycin and clarithromycin at the same concentration did not exert such effects. F-actin polymerization and Ca(++) influx induced by IP-10 and TARC in Th1 and Th2 cells, respectively, was down-regulated by RXM pretreatment. CONCLUSION These results imply that RXM exhibits bioregulatory function by influencing chemotaxis of Th1 and Th2 cells while leaving Treg cell migration unaffected.
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Affiliation(s)
- Taisuke Ito
- Department of Dermatology, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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Janson PCJ, Winerdal ME, Winqvist O. At the crossroads of T helper lineage commitment-Epigenetics points the way. Biochim Biophys Acta Gen Subj 2008; 1790:906-19. [PMID: 19162128 DOI: 10.1016/j.bbagen.2008.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 12/21/2022]
Abstract
The immune system has the capacity to respond to various types of pathogens including bacteria, viruses, tumors and parasites. This requires a flexible immune system, which in part depends on the development of alternative effector T helper cells, with different cytokine repertoires that direct the overall immune response. The reciprocal effects of the T helper subtypes Th1 and Th2 are well documented, but the mechanisms involved in alternative cytokine expression and silencing are less well defined. Introduction of advances within the field of chromatin folding and epigenetic regulation of transcription has begun to explain some of the fundamental principles of T helper cell development. In addition, epigenetic regulation has proven essential also for the more recently discovered T helper cell subtypes; regulatory T cells and the Th17 lineage. As the importance of proper epigenetic regulation becomes evident, attention is also focused on the potential harmfulness of epigenetic dysregulation. Autoimmunity and allergy are two clinical situations that have been implicated as results of imperfect cytokine silencing. This review will address recent advances in the field of epigenetic regulation of T lymphocytes and their maturation from naive cells into different effector T cell lineages. In particular, epigenetic involvement in regulation of key effector cytokines and specific transcription factors determining the CD4(+) T lymphocyte lineage commitment will be discussed.
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Affiliation(s)
- Peter C J Janson
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
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Tsuji-Takayama K, Suzuki M, Yamamoto M, Harashima A, Okochi A, Otani T, Inoue T, Sugimoto A, Toraya T, Takeuchi M, Yamasaki F, Nakamura S, Kibata M. The production of IL-10 by human regulatory T cells is enhanced by IL-2 through a STAT5-responsive intronic enhancer in the IL-10 locus. THE JOURNAL OF IMMUNOLOGY 2008; 181:3897-905. [PMID: 18768844 DOI: 10.4049/jimmunol.181.6.3897] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
STAT5 molecules are key components of the IL-2 signaling pathway, the deficiency of which often results in autoimmune pathology due to a reduced number of CD4(+)CD25(+) naturally occurring regulatory T (Treg) cells. One of the consequences of the IL-2-STAT5 signaling axis is up-regulation of FOXP3, a master control gene for naturally occurring Treg cells. However, the roles of STAT5 in other Treg subsets have not yet been elucidated. We recently demonstrated that IL-2 enhanced IL-10 production through STAT5 activation. This occurred in two types of human Treg cells: a novel type of umbilical cord blood-derived Treg cell, termed HOZOT, and Tr1-like Treg cells, IL-10-Treg. In this study, we examined the regulatory mechanisms of IL-10 production in these Treg cells, focusing specifically on the roles of STAT5. By performing bioinformatic analysis on the IL-10 locus, we identified one STAT-responsive element within intron 4, designated I-SRE-4, as an interspecies-conserved sequence. We found that I-SRE-4 acted as an enhancer element, and clustered CpGs around the I-SRE-4 were hypomethylated in IL-10-producing Treg cells, but not in other T cells. A gel-shift analysis using a nuclear extract from IL-2-stimulated HOZOT confirmed that CpG DNA methylation around I-SRE-4 reduced STAT5 binding to the element. Chromatin immunoprecipitation analysis revealed the in situ binding of IL-2-activated STAT5 to I-SRE-4. Thus, we provide molecular evidence for the involvement of an IL-2-STAT5 signaling axis in the expression of IL-10 by human Treg cells, an axis that is regulated by the intronic enhancer, I-SRE-4, and epigenetic modification of this element.
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Affiliation(s)
- Kazue Tsuji-Takayama
- Cell Biology Institute, Research Center, Hayashibara Biochemical Laboratories, Fujisaki, Okayama, Japan
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