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Peng XP, Caballero-Oteyza A, Grimbacher B. Common Variable Immunodeficiency: More Pathways than Roads to Rome. ANNUAL REVIEW OF PATHOLOGY 2023; 18:283-310. [PMID: 36266261 DOI: 10.1146/annurev-pathmechdis-031521-024229] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fifty years have elapsed since the term common variable immunodeficiency (CVID) was introduced to accommodate the many and varied antibody deficiencies being identified in patients with suspected inborn errors of immunity (IEIs). Since then, how the term is understood and applied for diagnosis and management has undergone many revisions, though controversy persists on how exactly to define and classify CVID. Many monogenic disorders have been added under its aegis, while investigations into polygenic, epigenetic, and somatic contributions to CVID susceptibility have gained momentum. Expansion of the overall IEI landscape has increasingly revealed genotypic and phenotypic overlap between CVID and various other immunological conditions, while increasingly routine genotyping of CVID patients continues to identify an incredible diversity of pathophysiological mechanisms affecting even single genes. Though many questions remain to be answered, the lessons we have already learned from CVID biology have greatly informed our understanding of adaptive, but also innate, immunity.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany; .,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrés Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany; .,Resolving Infection Susceptibility (RESIST) Cluster of Excellence, Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany; .,Resolving Infection Susceptibility (RESIST) Cluster of Excellence, Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany.,German Center for Infection Research (DZIF), Satellite Center Freiburg, Freiburg, Germany
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2
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Harley ITW, Allison K, Scofield RH. Polygenic autoimmune disease risk alleles impacting B cell tolerance act in concert across shared molecular networks in mouse and in humans. Front Immunol 2022; 13:953439. [PMID: 36090990 PMCID: PMC9450536 DOI: 10.3389/fimmu.2022.953439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Most B cells produced in the bone marrow have some level of autoreactivity. Despite efforts of central tolerance to eliminate these cells, many escape to periphery, where in healthy individuals, they are rendered functionally non-responsive to restimulation through their antigen receptor via a process termed anergy. Broad repertoire autoreactivity may reflect the chances of generating autoreactivity by stochastic use of germline immunoglobulin gene segments or active mechanisms may select autoreactive cells during egress to the naïve peripheral B cell pool. Likewise, it is unclear why in some individuals autoreactive B cell clones become activated and drive pathophysiologic changes in autoimmune diseases. Both of these remain central questions in the study of the immune system(s). In most individuals, autoimmune diseases arise from complex interplay of genetic risk factors and environmental influences. Advances in genome sequencing and increased statistical power from large autoimmune disease cohorts has led to identification of more than 200 autoimmune disease risk loci. It has been observed that autoantibodies are detectable in the serum years to decades prior to the diagnosis of autoimmune disease. Thus, current models hold that genetic defects in the pathways that control autoreactive B cell tolerance set genetic liability thresholds across multiple autoimmune diseases. Despite the fact these seminal concepts were developed in animal (especially murine) models of autoimmune disease, some perceive a disconnect between human risk alleles and those identified in murine models of autoimmune disease. Here, we synthesize the current state of the art in our understanding of human risk alleles in two prototypical autoimmune diseases – systemic lupus erythematosus (SLE) and type 1 diabetes (T1D) along with spontaneous murine disease models. We compare these risk networks to those reported in murine models of these diseases, focusing on pathways relevant to anergy and central tolerance. We highlight some differences between murine and human environmental and genetic factors that may impact autoimmune disease development and expression and may, in turn, explain some of this discrepancy. Finally, we show that there is substantial overlap between the molecular networks that define these disease states across species. Our synthesis and analysis of the current state of the field are consistent with the idea that the same molecular networks are perturbed in murine and human autoimmune disease. Based on these analyses, we anticipate that murine autoimmune disease models will continue to yield novel insights into how best to diagnose, prognose, prevent and treat human autoimmune diseases.
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Affiliation(s)
- Isaac T. W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
- Rheumatology Section, Medicine Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
- *Correspondence: Isaac T. W. Harley,
| | - Kristen Allison
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
| | - R. Hal Scofield
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Medical/Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
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3
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Hua L, Zhang Q, Zhu X, Wang R, You Q, Wang L. Beyond Proteolysis-Targeting Chimeric Molecules: Designing Heterobifunctional Molecules Based on Functional Effectors. J Med Chem 2022; 65:8091-8112. [PMID: 35686733 DOI: 10.1021/acs.jmedchem.2c00316] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, with the successful development of proteolysis-targeting chimeric molecules (PROTACs), the potential of heterobifunctional molecules to contribute to reenvisioning drug design, especially small-molecule drugs, has been increasingly recognized. Inspired by PROTACs, diverse heterobifunctional molecules have been reported to simultaneously bind two or more molecules and bring them into proximity to interaction, such as ribonuclease-recruiting, autophagy-recruiting, lysosome-recruiting, kinase-recruiting, phosphatase-recruiting, glycosyltransferase-recruiting, and acetyltransferase-recruiting chimeras. On the basis of the heterobifunctional principle, more opportunities for advancing drug design by linking potential effectors to a protein of interest (POI) have emerged. Herein, we introduce heterobifunctional molecules other than PROTACs, summarize the limitations of existing molecules, list the main challenges, and propose perspectives for future research directions, providing insight into alternative design strategies based on substrate-proximity-based targeting.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Xinyue Zhu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Ruoning Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, P. R. China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, P. R.China
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4
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Wang WW, Chen LY, Wozniak JM, Jadhav AM, Anderson H, Malone TE, Parker CG. Targeted Protein Acetylation in Cells Using Heterobifunctional Molecules. J Am Chem Soc 2021; 143:16700-16708. [PMID: 34592107 PMCID: PMC10793965 DOI: 10.1021/jacs.1c07850] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein acetylation is a central event in orchestrating diverse cellular processes. However, current strategies to investigate protein acetylation in cells are often nonspecific or lack temporal and magnitude control. Here, we developed an acetylation tagging system, AceTAG, to induce acetylation of targeted proteins. The AceTAG system utilizes bifunctional molecules to direct the lysine acetyltransferase p300/CBP to proteins fused with the small protein tag FKBP12F36V, resulting in their induced acetylation. Using AceTAG, we induced targeted acetylation of a diverse array of proteins in cells, specifically histone H3.3, the NF-κB subunit p65/RelA, and the tumor suppressor p53. We demonstrate that targeted acetylation with the AceTAG system is rapid, selective, reversible and can be controlled in a dose-dependent fashion. AceTAG represents a useful strategy to modulate protein acetylation and should enable the exploration of targeted acetylation in basic biological and therapeutic contexts.
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Affiliation(s)
- Wesley W Wang
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Appaso M Jadhav
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hayden Anderson
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Taylor E Malone
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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5
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Immunometabolism in systemic lupus erythematosus: Relevant pathogenetic mechanisms and potential clinical applications. J Formos Med Assoc 2021; 120:1667-1675. [PMID: 33836940 DOI: 10.1016/j.jfma.2021.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex, heterogeneous, systemic autoimmune disease involving a wide array of aberrant innate and adaptive immune responses. The immune microenvironment of SLE promotes the metabolic reprogramming of immune cells, leading to immune dyshomeostasis and triggering autoimmune inflammation. Different immune subsets switch from a resting state to a highly metabolic active state by alternating the redox-sensitive signaling pathway and the involved metabolic intermediates to amplify the inflammatory response, which is critical in SLE pathogenesis. In this review, we discuss abnormal metabolic changes in glucose metabolism, tricarboxylic acid cycle, and lipid and amino acid metabolism as well as mitochondrial dysfunction in immune cells in SLE. We also review studies focused on the potential targets for key molecules of metabolic pathways in SLE, such as hypoxia-inducible factor-1α, mammalian target of rapamycin, and AMP-activated protein kinase. We highlight the therapeutic rationale for targeting these pathways in treating SLE and summarize their recent clinical applications in SLE.
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6
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Wu H, Chang C, Lu Q. The Epigenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:185-207. [PMID: 32445096 DOI: 10.1007/978-981-15-3449-2_7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a life-threatening autoimmune disease that is characterized by dysregulated dendritic cells, T and B cells, and abundant autoantibodies. The pathogenesis of lupus remains unclear. However, increasing evidence has shown that environment factors, genetic susceptibilities, and epigenetic regulation contribute to abnormalities in the immune system. In the past decades, several risk gene loci have been identified, such as MHC and C1q. However, genetics cannot explain the high discordance of lupus incidence in homozygous twins. Environmental factor-induced epigenetic modifications on immune cells may provide some insight. Epigenetics refers to inheritable changes in a chromosome without altering DNA sequence. The primary mechanisms of epigenetics include DNA methylation, histone modifications, and non-coding RNA regulations. Increasing evidence has shown the importance of dysregulated epigenetic modifications in immune cells in pathogenesis of lupus, and has identified epigenetic changes as potential biomarkers and therapeutic targets. Environmental factors, such as drugs, diet, and pollution, may also be the triggers of epigenetic changes. Therefore, this chapter will summarize the up-to-date progress on epigenetics regulation in lupus, in order to broaden our understanding of lupus and discuss the potential roles of epigenetic regulations for clinical applications.
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Affiliation(s)
- Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Christopher Chang
- Division of Pediatric Immunology and Allergy, Joe DiMaggio Children's Hospital, Hollywood, FL, 33021, USA.,Division of Rheumatology, Allergy and Clinical Immunology, University of California Davis, Davis, CA, 95616, USA
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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7
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Wu H, Chen Y, Zhu H, Zhao M, Lu Q. The Pathogenic Role of Dysregulated Epigenetic Modifications in Autoimmune Diseases. Front Immunol 2019; 10:2305. [PMID: 31611879 PMCID: PMC6776919 DOI: 10.3389/fimmu.2019.02305] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022] Open
Abstract
Autoimmune diseases can be chronic with relapse of inflammatory symptoms, but it can be also acute and life-threatening if immune cells destroy life-supporting organs, such as lupus nephritis. The etiopathogenesis of autoimmune diseases has been revealed as that genetics and environmental factors-mediated dysregulated immune responses contribute to the initiation and development of autoimmune disorders. However, the current understanding of pathogenesis is limited and the underlying mechanism has not been well defined, which lows the development of novel biomarkers and new therapeutic strategies for autoimmune diseases. To improve this, broadening and deepening our understanding of pathogenesis is an unmet need. As genetic susceptibility cannot explain the low accordance rate of incidence in homozygous twins, epigenetic regulations might be an additional explanation. Therefore, this review will summarize current progress of studies on epigenetic dysregulations contributing to autoimmune diseases, including SLE, rheumatoid arthritis (RA), psoriasis, type 1 diabetes (T1D), and systemic sclerosis (SSc), hopefully providing opinions on orientation of future research, as well as discussing the clinical utilization of potential biomarkers and therapeutic strategies for these diseases.
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Affiliation(s)
- Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yongjian Chen
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Huan Zhu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
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8
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Fang F, Li G, Jing M, Xu L, Li Z, Li M, Yang C, Liu Y, Qian G, Hu X, Li G, Xie Y, Feng C, Li X, Pan J, Li Y, Feng X, Li Y. C646 modulates inflammatory response and antibacterial activity of macrophage. Int Immunopharmacol 2019; 74:105736. [PMID: 31302452 DOI: 10.1016/j.intimp.2019.105736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 06/08/2019] [Accepted: 06/29/2019] [Indexed: 12/26/2022]
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9
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Tirosh I, Spielman S, Barel O, Ram R, Stauber T, Paret G, Rubinsthein M, Pessach IM, Gerstein M, Anikster Y, Shukrun R, Dagan A, Adler K, Pode-Shakked B, Volkov A, Perelman M, Greenberger S, Somech R, Lahav E, Majmundar AJ, Padeh S, Hildebrandt F, Vivante A. Whole exome sequencing in childhood-onset lupus frequently detects single gene etiologies. Pediatr Rheumatol Online J 2019; 17:52. [PMID: 31362757 PMCID: PMC6668194 DOI: 10.1186/s12969-019-0349-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) comprise a diverse range of clinical manifestations. To date, more than 30 single gene causes of lupus/lupus like syndromes in humans have been identified. In the clinical setting, identifying the underlying molecular diagnosis is challenging due to phenotypic and genetic heterogeneity. METHODS We employed whole exome sequencing (WES) in patients presenting with childhood-onset lupus with severe and/or atypical presentations to identify cases that are explained by a single-gene (monogenic) cause. RESULTS From January 2015 to June 2018 15 new cases of childhood-onset SLE were diagnosed in Edmond and Lily Safra Children's Hospital. By WES we identified causative mutations in four subjects in five different genes: C1QC, SLC7A7, MAN2B1, PTEN and STAT1. No molecular diagnoses were established on clinical grounds prior to genetic testing. CONCLUSIONS We identified a significant fraction of monogenic SLE etiologies using WES and confirm the genetic locus heterogeneity in childhood-onset lupus. These results highlight the importance of establishing a genetic diagnosis for children with severe or atypical lupus by providing accurate and early etiology-based diagnoses and improving subsequent clinical management.
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Affiliation(s)
- Irit Tirosh
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0001 2107 2845grid.413795.dRheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shiri Spielman
- 0000 0001 2107 2845grid.413795.dRheumatology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ortal Barel
- 0000 0001 2107 2845grid.413795.dThe Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Reut Ram
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel
| | - Tali Stauber
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gideon Paret
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marina Rubinsthein
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Itai M. Pessach
- 0000 0001 2107 2845grid.413795.dIntensive care unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Maya Gerstein
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Yair Anikster
- 0000 0001 2107 2845grid.413795.dMetabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Shukrun
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Adi Dagan
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Katerina Adler
- 0000 0001 2107 2845grid.413795.dThe Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ben Pode-Shakked
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0001 2107 2845grid.413795.dMetabolic Disease Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Alexander Volkov
- 0000 0001 2107 2845grid.413795.dPathology Department, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Marina Perelman
- 0000 0001 2107 2845grid.413795.dPathology Department, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shoshana Greenberger
- 0000 0001 2107 2845grid.413795.dDepartment of Dermatology, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Raz Somech
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Einat Lahav
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics A Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel-Hashomer, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel ,0000 0001 2107 2845grid.413795.dNephrology Unit, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601 Ramat Gan, Israel
| | - Amar J. Majmundar
- 000000041936754Xgrid.38142.3cDivision of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Shai Padeh
- 0000 0001 2107 2845grid.413795.dDepartment of Pediatrics B, Edmond and Lily Safra Children’s Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601 Ramat Gan, Israel ,0000 0004 1937 0546grid.12136.37Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Friedhelm Hildebrandt
- 000000041936754Xgrid.38142.3cDivision of Nephrology, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA USA
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel. .,Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.
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10
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Wang Z, Long H, Chang C, Zhao M, Lu Q. Crosstalk between metabolism and epigenetic modifications in autoimmune diseases: a comprehensive overview. Cell Mol Life Sci 2018; 75:3353-3369. [PMID: 29974127 PMCID: PMC11105184 DOI: 10.1007/s00018-018-2864-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Little information is available regarding mechanistic links between epigenetic modifications and autoimmune diseases. It seems plausible to surmise that aberrant gene expression and energy metabolism would disrupt immune tolerance, which could ultimately result in autoimmune responses. Metaboloepigenetics is an emerging paradigm that defines the interrelationships between metabolism and epigenetics. Epigenetic modifications, such as the methylation/demethylation of DNA and histone proteins and histone acetylation/deacetylation can be dynamically produced and eliminated by a group of enzymes that consume several metabolites derived from various physiological pathways. Recent insights into cellular metabolism have demonstrated that environmental stimuli such as dietary exposure and nutritional status act through the variation in concentration of metabolites to affect epigenetic regulation and breakdown biochemical homeostasis. Metabolites, including S-adenosylmethionine, acetyl-CoA, nicotinamide adenine dinucleotide, α-ketoglutarate, and ATP serve as cofactors for chromatin-modifying enzymes, such as methyltransferases, deacetylases and kinases, which are responsible for chromatin remodelling. The concentration of crucial nutrients, such as glucose, glutamine, and oxygen, spatially and temporally modulate epigenetic modifications to regulate gene expression and the reaction to stressful microenvironments in disease pathology. In this review, we focus on the interaction between metabolic intermediates and epigenetic modifications, integrating environmental signals with programmes through modification of the epigenome-metabolome to speculate as to how this may influence autoimmune diseases.
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Affiliation(s)
- Zijun Wang
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, No. 139 Renmin Middle Rd, Changsha, 410011, Hunan, China
| | - Hai Long
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, No. 139 Renmin Middle Rd, Changsha, 410011, Hunan, China
| | - Christopher Chang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Suite 6510, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Ming Zhao
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, No. 139 Renmin Middle Rd, Changsha, 410011, Hunan, China.
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, No. 139 Renmin Middle Rd, Changsha, 410011, Hunan, China.
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Ulff-Møller CJ, Asmar F, Liu Y, Svendsen AJ, Busato F, Grønbaek K, Tost J, Jacobsen S. Twin DNA Methylation Profiling Reveals Flare-Dependent Interferon Signature and B Cell Promoter Hypermethylation in Systemic Lupus Erythematosus. Arthritis Rheumatol 2018; 70:878-890. [PMID: 29361205 DOI: 10.1002/art.40422] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 01/17/2018] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) has limited monozygotic twin concordance, implying a role for pathogenic factors other than genetic variation, such as epigenetic changes. Using the disease-discordant twin model, we investigated genome-wide DNA methylation changes in sorted CD4+ T cells, monocytes, granulocytes, and B cells in twin pairs with at least 1 SLE-affected twin. METHODS Peripheral blood obtained from 15 SLE-affected twin pairs (6 monozygotic and 9 dizygotic) was processed using density-gradient centrifugation for the granulocyte fraction. CD4+ T cells, monocytes, and B cells were further isolated using magnetic beads. Genome-wide DNA methylation was analyzed using Infinium HumanMethylation450K BeadChips. When comparing probes from SLE-affected twins and co-twins, differential DNA methylation was considered statistically significant when the P value was less than 0.01 and biologically relevant when the median DNA methylation difference was >7%. Findings were validated by pyrosequencing and replicated in an independent case-control sample. RESULTS In paired analyses of twins discordant for SLE restricted to the gene promoter and start region, we identified 55, 327, 247, and 1,628 genes with differentially methylated CpGs in CD4+ T cells, monocytes, granulocytes, and B cells, respectively. All cell types displayed marked hypomethylation in interferon-regulated genes, such as IFI44L, PARP9, and IFITM1, which was more pronounced in twins who experienced a disease flare within the past 2 years. In contrast to what was observed in the other cell types, differentially methylated CpGs in B cells were predominantly hypermethylated, and the most important upstream regulators included TNF and EP300. CONCLUSION Hypomethylation of interferon-regulated genes occurs in all major cellular compartments in SLE-affected twins. The observed B cell promoter hypermethylation is a novel finding with potential significance in SLE pathogenesis.
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Affiliation(s)
- Constance J Ulff-Møller
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark, and Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | | | - Yi Liu
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | | | - Florence Busato
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | - Kirsten Grønbaek
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
| | - Jörg Tost
- Commissariat à l'énergie atomique et aux énergies alternatives, Institut de Biologie Francois Jacob, Evry, France
| | - Søren Jacobsen
- Rigshospitalet and University of Copenhagen, Copenhagen, Denmark
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12
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Arts RJW, Joosten LAB, Netea MG. The Potential Role of Trained Immunity in Autoimmune and Autoinflammatory Disorders. Front Immunol 2018. [PMID: 29515591 PMCID: PMC5826224 DOI: 10.3389/fimmu.2018.00298] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During induction of trained immunity, monocytes and macrophages undergo a functional and transcriptional reprogramming toward increased activation. Important rewiring of cellular metabolism of the myeloid cells takes place during induction of trained immunity, including a shift toward glycolysis induced through the mTOR pathway, as well as glutaminolysis and cholesterol synthesis. Subsequently, this leads to modulation of the function of epigenetic enzymes, resulting in important changes in chromatin architecture that enables increased gene transcription. However, in addition to the beneficial effects of trained immunity as a host defense mechanism, we hypothesize that trained immunity also plays a deleterious role in the induction and/or maintenance of autoimmune and autoinflammatory diseases if inappropriately activated.
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Affiliation(s)
- Rob J W Arts
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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13
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Epigenetic regulation in B-cell maturation and its dysregulation in autoimmunity. Cell Mol Immunol 2018; 15:676-684. [PMID: 29375128 PMCID: PMC6123482 DOI: 10.1038/cmi.2017.133] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 12/11/2022] Open
Abstract
B cells have a critical role in the initiation and acceleration of autoimmune diseases, especially those mediated by autoantibodies. In the peripheral lymphoid system, mature B cells are activated by self or/and foreign antigens and signals from helper T cells for differentiating into either memory B cells or antibody-producing plasma cells. Accumulating evidence has shown that epigenetic regulations modulate somatic hypermutation and class switch DNA recombination during B-cell activation and differentiation. Any abnormalities in these complex regulatory processes may contribute to aberrant antibody production, resulting in autoimmune pathogenesis such as systemic lupus erythematosus. Newly generated knowledge from advanced modern technologies such as next-generation sequencing, single-cell sequencing and DNA methylation sequencing has enabled us to better understand B-cell biology and its role in autoimmune development. Thus this review aims to summarize current research progress in epigenetic modifications contributing to B-cell activation and differentiation, especially under autoimmune conditions such as lupus, rheumatoid arthritis and type 1 diabetes.
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14
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Pazhouhandeh M, Sahraian MA, Siadat SD, Fateh A, Vaziri F, Tabrizi F, Ajorloo F, Arshadi AK, Fatemi E, Piri Gavgani S, Mahboudi F, Rahimi Jamnani F. A systems medicine approach reveals disordered immune system and lipid metabolism in multiple sclerosis patients. Clin Exp Immunol 2018; 192:18-32. [PMID: 29194580 DOI: 10.1111/cei.13087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Identification of autoimmune processes and introduction of new autoantigens involved in the pathogenesis of multiple sclerosis (MS) can be helpful in the design of new drugs to prevent unresponsiveness and side effects in patients. To find significant changes, we evaluated the autoantibody repertoires in newly diagnosed relapsing-remitting MS patients (NDP) and those receiving disease-modifying therapy (RP). Through a random peptide phage library, a panel of NDP- and RP-specific peptides was identified, producing two protein data sets visualized using Gephi, based on protein--protein interactions in the STRING database. The top modules of NDP and RP networks were assessed using Enrichr. Based on the findings, a set of proteins, including ATP binding cassette subfamily C member 1 (ABCC1), neurogenic locus notch homologue protein 1 (NOTCH1), hepatocyte growth factor receptor (MET), RAF proto-oncogene serine/threonine-protein kinase (RAF1) and proto-oncogene vav (VAV1) was found in NDP and was involved in over-represented terms correlated with cell-mediated immunity and cancer. In contrast, transcription factor RelB (RELB), histone acetyltransferase p300 (EP300), acetyl-CoA carboxylase 2 (ACACB), adiponectin (ADIPOQ) and phosphoenolpyruvate carboxykinase 2 mitochondrial (PCK2) had major contributions to viral infections and lipid metabolism as significant events in RP. According to these findings, further research is required to demonstrate the pathogenic roles of such proteins and autoantibodies targeting them in MS and to develop therapeutic agents which can ameliorate disease severity.
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Affiliation(s)
- M Pazhouhandeh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - M-A Sahraian
- MS Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - S D Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - A Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Tabrizi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Ajorloo
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, Islamic Azad University, East Tehran Branch, Tehran, Iran
| | - A K Arshadi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - E Fatemi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S Piri Gavgani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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15
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Németh T, Mócsai A, Lowell CA. Neutrophils in animal models of autoimmune disease. Semin Immunol 2016; 28:174-86. [PMID: 27067180 DOI: 10.1016/j.smim.2016.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/21/2023]
Abstract
Neutrophils have traditionally been thought to play only a peripheral role in the genesis of many autoimmune and inflammatory diseases. However, recent studies in a variety of animal models suggest that these cells are central to the initiation and propagation of autoimmunity. The use of mouse models, which allow either deletion of neutrophils or the targeting of specific neutrophil functions, has revealed the many complex ways these cells contribute to autoimmune/inflammatory processes. This includes generation of self antigens through the process of NETosis, regulation of T-cell and dendritic cell activation, production of cytokines such as BAFF that stimulate self-reactive B-cells, as well as indirect effects on epithelial cell stability. In comparing the many different autoimmune models in which neutrophils have been examined, a number of common underlying themes emerge - such as a role for neutrophils in stimulating vascular permeability in arthritis, encephalitis and colitis. The use of animal models has also stimulated the development of new therapeutics that target neutrophil functions, such as NETosis, that may prove beneficial in human disease. This review will summarize neutrophil contributions in a number of murine autoimmune/inflammatory disease models.
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Affiliation(s)
- Tamás Németh
- Department of Physiology, Semmelweis University School of Medicine, 1094 Budapest, Hungary; MTA-SE "Lendület" Inflammation Physiology Research Group of the Hungarian Academy of Sciences and Semmelweis University, 1094 Budapest, Hungary
| | - Attila Mócsai
- Department of Physiology, Semmelweis University School of Medicine, 1094 Budapest, Hungary; MTA-SE "Lendület" Inflammation Physiology Research Group of the Hungarian Academy of Sciences and Semmelweis University, 1094 Budapest, Hungary
| | - Clifford A Lowell
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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16
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Abstract
Our understanding of epigenetics in complex diseases is rapidly advancing and increasingly influencing the practice of medicine. Much is known about disruption of chromatin-modifying enzymes in malignant disease, but knowledge of irregular epigenetics in immune-driven disorders is just emerging. Epigenetic factors, such as DNA or histone modifications, are indispensable for precise gene expression in diverse immune cell types. Thus a disruption of epigenetic landscapes likely has a large impact on immune homeostasis. Moreover, the low concordance rates for most autoimmune diseases suggest that epigenetics contribute to immune tolerance disturbance. Here we review the important role of epigenetics for initiation, maintenance, tolerance, and training of immune responses. We discuss evolving evidence that DNA/histone modifications and chromatin-modifying enzymes are altered in immune-based diseases. Furthermore, we explore the potential of small molecules targeting epigenetic machinery, some of which are already used in oncology, as a way to reset the immune response in disease.
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17
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Zan H, Casali P. Epigenetics of Peripheral B-Cell Differentiation and the Antibody Response. Front Immunol 2015; 6:631. [PMID: 26697022 PMCID: PMC4677338 DOI: 10.3389/fimmu.2015.00631] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone post-translational modifications, DNA methylation, and alteration of gene expression by non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are heritable changes that are independent from the genomic DNA sequence. These regulate gene activities and, therefore, cellular functions. Epigenetic modifications act in concert with transcription factors and play critical roles in B cell development and differentiation, thereby modulating antibody responses to foreign- and self-antigens. Upon antigen encounter by mature B cells in the periphery, alterations of these lymphocytes epigenetic landscape are induced by the same stimuli that drive the antibody response. Such alterations instruct B cells to undergo immunoglobulin (Ig) class switch DNA recombination (CSR) and somatic hypermutation (SHM), as well as differentiation to memory B cells or long-lived plasma cells for the immune memory. Inducible histone modifications, together with DNA methylation and miRNAs modulate the transcriptome, particularly the expression of activation-induced cytidine deaminase, which is essential for CSR and SHM, and factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1. These inducible B cell-intrinsic epigenetic marks guide the maturation of antibody responses. Combinatorial histone modifications also function as histone codes to target CSR and, possibly, SHM machinery to the Ig loci by recruiting specific adaptors that can stabilize CSR/SHM factors. In addition, lncRNAs, such as recently reported lncRNA-CSR and an lncRNA generated through transcription of the S region that form G-quadruplex structures, are also important for CSR targeting. Epigenetic dysregulation in B cells, including the aberrant expression of non-coding RNAs and alterations of histone modifications and DNA methylation, can result in aberrant antibody responses to foreign antigens, such as those on microbial pathogens, and generation of pathogenic autoantibodies, IgE in allergic reactions, as well as B cell neoplasia. Epigenetic marks would be attractive targets for new therapeutics for autoimmune and allergic diseases, and B cell malignancies.
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Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Paolo Casali
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
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18
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Abstract
Systemic lupus erythematosus is a prototypic autoimmune disease characterized by the production of an array of pathogenic autoantibodies, including high-affinity anti-dsDNA IgG antibodies, which play an important role in disease development and progression. Lupus preferentially affects women during their reproductive years. The pathogenesis of lupus is contributed by both genetic factors and epigenetic modifications that arise from exposure to the environment. Epigenetic marks, including DNA methylation, histone post-translational modifications and microRNAs (miRNAs), interact with genetic programs to regulate immune responses. Epigenetic modifications influence gene expression and modulate B cell functions, such as class-switch DNA recombination, somatic hypermutation and plasma cell differentiation, thereby informing the antibody response. Epigenetic dysregulation can result in aberrant antibody responses to exogenous antigens or self-antigens, such as chromatin, histones and dsDNA in lupus. miRNAs play key roles in the post-transcriptional regulation of most gene-regulatory pathways and regulate both the innate and adaptive immune responses. In mice, dysregulation of miRNAs leads to aberrant immune responses and development of systemic autoimmunity. Altered miRNA expression has been reported in human autoimmune diseases, including lupus. The dysregulation of miRNAs in lupus could be the result of multiple environmental factors, such as sex hormones and viral or bacterial infection. Modulation of miRNA is a potential therapeutic strategy for lupus.
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Affiliation(s)
- Hong Zan
- Department of Microbiology and Immunology, School of Medicine, University of Texas Health Science Center , San Antonio, TX , USA
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19
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Epigenetic Control of B Cell Development and B-Cell-Related Immune Disorders. Clin Rev Allergy Immunol 2015; 50:301-11. [DOI: 10.1007/s12016-015-8494-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Alberghini F, Petrocelli V, Rahmat M, Casola S. An epigenetic view of B‐cell disorders. Immunol Cell Biol 2015; 93:253-60. [DOI: 10.1038/icb.2014.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/06/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Mahshid Rahmat
- IFOM, The FIRC Institute of Molecular Oncology Foundation Milan Italy
| | - Stefano Casola
- IFOM, The FIRC Institute of Molecular Oncology Foundation Milan Italy
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21
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Good-Jacobson KL. Regulation of germinal center, B-cell memory, and plasma cell formation by histone modifiers. Front Immunol 2014; 5:596. [PMID: 25477884 PMCID: PMC4237133 DOI: 10.3389/fimmu.2014.00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/06/2014] [Indexed: 01/05/2023] Open
Abstract
Understanding the regulation of antibody production and B-cell memory formation and function is core to finding new treatments for B-cell-derived cancers, antibody-mediated autoimmune disorders, and immunodeficiencies. Progression from a small number of antigen-specific B-cells to the production of a large number of antibody-secreting cells is tightly regulated. Although much progress has been made in revealing the transcriptional regulation of B-cell differentiation that occurs during humoral immune responses, there are still many questions that remain unanswered. Recent work on the expression and roles of histone modifiers in lymphocytes has begun to shed light on this additional level of regulation. This review will discuss the recent advancements in understanding how humoral immune responses, in particular germinal centers and memory cells, are modulated by histone modifiers.
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Affiliation(s)
- Kim L Good-Jacobson
- Immunology Division, Walter and Eliza Hall Institute of Medical Research , Parkville, VIC , Australia ; Department of Medical Biology, University of Melbourne , Parkville, VIC , Australia
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22
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Pieterse E, van der Vlag J. Breaking immunological tolerance in systemic lupus erythematosus. Front Immunol 2014; 5:164. [PMID: 24782867 PMCID: PMC3988363 DOI: 10.3389/fimmu.2014.00164] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/28/2014] [Indexed: 12/31/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a fairly heterogeneous autoimmune disease of unknown etiology that mainly affects women in the childbearing age. SLE is a prototype type III hypersensitivity reaction in which immune complex depositions cause inflammation and tissue damage in multiple organs. Two distinct cell death pathways, apoptosis and NETosis, gained a great deal of interest among scientists, since both processes seem to be deregulated in SLE. There is growing evidence that histone modifications induced by these cell death pathways exert a central role in the induction of autoimmunity. In the current review, we discuss how abnormalities in apoptosis, NETosis, and histone modifications may lead to a break of immunological tolerance in SLE.
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Affiliation(s)
- Elmar Pieterse
- Department of Nephrology, Radboud University Medical Center , Nijmegen , Netherlands
| | - Johan van der Vlag
- Department of Nephrology, Radboud University Medical Center , Nijmegen , Netherlands
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23
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Abstract
Epigenetic mechanisms are proposed to underlie aberrant gene expression in systemic lupus erythematosus (SLE) that results in dysregulation of the immune system and loss of tolerance. Modifications of DNA and histones require substrates derived from diet and intermediary metabolism. DNA and histone methyltransferases depend on S-adenosylmethionine (SAM) as a methyl donor. SAM is generated from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase (MAT), a redox-sensitive enzyme in the SAM cycle. The availability of B vitamins and methionine regulate SAM generation. The DNA of SLE patients is hypomethylated, indicating dysfunction in the SAM cycle and methyltransferase activity. Acetyl-CoA, which is necessary for histone acetylation, is generated from citrate produced in mitochondria. Mitochondria are also responsible for de novo synthesis of flavin adenine dinucleotide (FAD) for histone demethylation. Mitochondrial oxidative phosphorylation is the dominant source of ATP. The depletion of ATP in lupus T cells may affect MAT activity as well as adenosine monophosphate (AMP) activated protein kinase (AMPK), which phosphorylates histones and inhibits mechanistic target of rapamycin (mTOR). In turn, mTOR can modify epigenetic pathways including methylation, demethylation, and histone phosphorylation and mediates enhanced T-cell activation in SLE. Beyond their role in metabolism, mitochondria are the main source of reactive oxygen intermediates (ROI), which activate mTOR and regulate the activity of histone and DNA modifying enzymes. In this review we will focus on the sources of metabolites required for epigenetic regulation and how the flux of the underlying metabolic pathways affects gene expression.
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Affiliation(s)
- Zachary Oaks
- Division of Rheumatology, Departments of Medicine, Microbiology and Immunology, and Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, College of Medicine , Syracuse, NY , USA
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Li G, Zan H, Xu Z, Casali P. Epigenetics of the antibody response. Trends Immunol 2013; 34:460-70. [PMID: 23643790 PMCID: PMC3744588 DOI: 10.1016/j.it.2013.03.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 03/26/2013] [Accepted: 03/28/2013] [Indexed: 12/19/2022]
Abstract
Epigenetic marks, such as DNA methylation, histone post-translational modifications and miRNAs, are induced in B cells by the same stimuli that drive the antibody response. They play major roles in regulating somatic hypermutation (SHM), class switch DNA recombination (CSR), and differentiation to plasma cells or long-lived memory B cells. Histone modifications target the CSR and, possibly, SHM machinery to the immunoglobulin locus; they together with DNA methylation and miRNAs modulate the expression of critical elements of that machinery, such as activation-induced cytidine deaminase (AID), as well as factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1 (Blimp-1). These inducible B cell-intrinsic epigenetic marks instruct the maturation of antibody responses. Their dysregulation plays an important role in aberrant antibody responses to foreign antigens, such as those of microbial pathogens, and self-antigens, such as those targeted in autoimmunity, and B cell neoplasia.
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Affiliation(s)
- Guideng Li
- Institute for Immunology and School of Medicine, University of California, Irvine, CA 92697-4120, USA
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25
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Knoechel B, Lohr JG. Genomics of lymphoid malignancies reveal major activation pathways in lymphocytes. J Autoimmun 2013; 45:15-23. [PMID: 23880067 DOI: 10.1016/j.jaut.2013.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 06/19/2013] [Indexed: 01/21/2023]
Abstract
Breakdown of tolerance leads to autoimmunity due to emergence of autoreactive T or B cell clones. Autoimmune diseases predispose to lymphoid malignancies and lymphoid malignancies, conversely, can manifest as autoimmune diseases. While it has been clear for a long time that a competitive advantage and uncontrolled growth of lymphocytes contribute to the pathogenesis of both lymphoid malignancies as well as autoimmune diseases, the overlap of the underlying mechanisms has been less well described. Next generation sequencing has led to massive expansion of the available genomic data in many diseases over the last five years. These data allow for comparison of the molecular pathogenesis between autoimmune diseases and lymphoid malignancies. Here, we review the similarities between autoimmune diseases and lymphoid malignancies: 1) Both, autoimmune diseases and lymphoid malignancies are characterized by activation of the same T and B cell signaling pathways, and dysregulation of these pathways can occur through genetic or epigenetic events. 2) In both scenarios, clonal and subclonal evolution of lymphocytes contribute to disease. 3) Development of both diseases not only depends on T or B cell intrinsic factors, such as germline or somatic mutations, but also on environmental factors. These include infections, the presence of other immune cells in the microenvironment, and the cytokine milieu. A better mechanistic understanding of the parallels between lymphomagenesis and autoimmunity may help the development of precision treatment strategies with rationally designed therapeutic agents.
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Affiliation(s)
- Birgit Knoechel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
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26
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The applied basic research of systemic lupus erythematosus based on the biological omics. Genes Immun 2013; 14:133-46. [PMID: 23446742 DOI: 10.1038/gene.2013.3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the production of autoantibodies directed against nuclear self-antigens and circulating immune complexes. This results in damages to various organs or systems, including skin, joints, kidneys and the central nervous system. Clinical manifestations of SLE could be diverse, including glomerulonephritis, dermatitis, thrombosis, vasculitis, seizures and arthritis. The complicated pathogenesis and varied clinical symptoms of SLE pose great challenges in the diagnosis and monitoring of this disease. Unfortunately, the etiological factors and pathogenesis of SLE are still not completely understood. It is noteworthy that recent advances in our understanding of the biological omics and emerging technologies have been providing new tools in the analyses of SLE, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics and so on. In this article, we summarize our current knowledge in this field for a better understanding of the pathogenesis, diagnosis and treatment for SLE.
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27
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Liu CL, Tangsombatvisit S, Rosenberg JM, Mandelbaum G, Gillespie EC, Gozani OP, Alizadeh AA, Utz PJ. Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies. Arthritis Res Ther 2012; 14:R25. [PMID: 22300536 PMCID: PMC3392818 DOI: 10.1186/ar3707] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/22/2012] [Accepted: 02/02/2012] [Indexed: 02/05/2023] Open
Abstract
Introduction Autoreactivity to histones is a pervasive feature of several human autoimmune disorders, including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutrophil extracellular traps (NETs) may potentially drive the process by which tolerance to these chromatin-associated proteins is broken. We hypothesized that NETs and their unique histone PTMs might be capable of inducing autoantibodies that target histones. Methods We developed a novel and efficient method for the in vitro production, visualization, and broad profiling of histone-PTMs of human and murine NETs. We also immunized Balb/c mice with murine NETs and profiled their sera on autoantigen and histone peptide microarrays for evidence of autoantibody production to their immunogen. Results We confirmed specificity toward acetyl-modified histone H2B as well as to other histone PTMs in sera from patients with SLE known to have autoreactivity against histones. We observed enrichment for distinctive histone marks of transcriptionally silent DNA during NETosis triggered by diverse stimuli. However, NETs derived from human and murine sources did not harbor many of the PTMs toward which autoreactivity was observed in patients with SLE or in MRL/lpr mice. Further, while murine NETs were weak autoantigens in vivo, there was only partial overlap in the immunoglobulin G (IgG) and IgM autoantibody profiles induced by vaccination of mice with NETs and those seen in patients with SLE. Conclusions Isolated in vivo exposure to NETs is insufficient to break tolerance and may involve additional factors that have yet to be identified.
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Affiliation(s)
- Chih Long Liu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford School of Medicine, 269 Campus Drive, Stanford, California 94305, USA
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Devipriya B, Kumaradhas P. Probing the effect of intermolecular interaction and understanding the electrostatic moments of anacardic acid in the active site of p300 enzyme via DFT and charge density analysis. J Mol Graph Model 2011; 34:57-66. [PMID: 22306413 DOI: 10.1016/j.jmgm.2011.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/19/2011] [Accepted: 12/19/2011] [Indexed: 01/07/2023]
Abstract
A charge density analysis has been performed on gas phase and docked forms of anacardic acid molecule to understand its charge density distribution, electrostatic moments and the conformation in the active site of p300 enzyme. Here, we report the binding affinity of anacardic acid with the p300 enzyme calculated from docking analysis. The charge density distribution of anacardic acid molecule in the gas phase as well as the docked form has been determined from the high level quantum chemical calculations using HF and DFT methods coupled with AIM theory. The charge density study on both forms of anacardic acid differentiates its structural and the electrostatic properties in different environments. When the molecule enters into the active site of p300 its conformation, charge density distribution, dipole moment and electrostatic potential are significantly altered in comparison to its gas phase structure. In the active site, the molecule adopts different conformations, its pentadecyl chain is found to be highly twisted; the charges are redistributed and the dipole moment increases from 2.37 to 3.17D. Due to the charge redistribution, the electronegative region of carboxyl group increased as it is found small in the gas phase. The comparisons between both forms reveal the flexibility of anacardic acid in the active site.
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Affiliation(s)
- B Devipriya
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636011, India
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Hughes T, Sawalha AH. The role of epigenetic variation in the pathogenesis of systemic lupus erythematosus. Arthritis Res Ther 2011; 13:245. [PMID: 22044622 PMCID: PMC3308098 DOI: 10.1186/ar3484] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The focus of the present review is on the extent to which epigenetic alterations influence the development of systemic lupus erythematosus. Lupus is a systemic autoimmune disease characterized by the production of autoantibodies directed at nuclear self-antigens. A DNA methylation defect in CD4+ T cells has long been observed in idiopathic and drug-induced lupus. Recent studies utilizing high-throughput technologies have further characterized the nature of the DNA methylation defect in lupus CD4+ T cells. Emerging evidence in the literature is revealing an increasingly interconnected network of epigenetic dysregulation in lupus. Recent reports describe variable expression of a number of regulatory microRNAs in lupus CD4+ T cells, some of which govern the expression of DNA methyltransferase 1. While studies to date have revealed a significant role for epigenetic defects in the pathogenesis of lupus, the causal nature of epigenetic variation in lupus remains elusive. Future longitudinal epigenetic studies in lupus are therefore needed.
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Affiliation(s)
- Travis Hughes
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Amr H Sawalha
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
- 825 NE 13th Street, MS#24, Oklahoma City, OK 73104, USA
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Abstract
The etiology of autoimmune diseases remains largely unknown. Concordance rates in monozygotic twins are lower than 50% while genome-wide association studies propose numerous significant associations representing only a minority of patients. These lines of evidence strongly support other complementary mechanisms involved in the regulation of genes expression ultimately causing overt autoimmunity. Alterations in the post-translational modification of histones and DNA methylation are the two major epigenetic mechanisms that may potentially cause a breakdown of immune tolerance and the perpetuation of autoimmune diseases. In recent years, several studies both in clinical settings and experimental models proposed that the epigenome may hold the key to a better understanding of autoimmunity initiation and perpetuation. More specifically, data support the impact of epigenetic changes in systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis and other autoimmune diseases, in some cases based on mechanistical observations. We herein discuss what we currently know and what we expect will come in the next future. Ultimately, epigenetic treatments already being used in oncology may soon prove beneficial also in autoimmune diseases.
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Affiliation(s)
- Francesca Meda
- Department of Medicine and Hepatobiliary Immunopathology Unit, IRCCS Istituto Clinico Humanitas, Rozzano, Milan, Italy
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A New Epigenetic Challenge: Systemic Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 711:117-36. [DOI: 10.1007/978-1-4419-8216-2_9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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32
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Epigenetic regulation and the pathogenesis of systemic lupus erythematosus. Transl Res 2009; 153:4-10. [PMID: 19100952 DOI: 10.1016/j.trsl.2008.10.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 10/23/2008] [Accepted: 10/26/2008] [Indexed: 12/19/2022]
Abstract
The pathogenesis of systemic lupus erythematosus (SLE) is incompletely understood. Studies in both lupus animal models and human disease indicate a clear role for epigenetic defects, particularly DNA methylation, in the pathogenesis of lupus. T-cell DNA from active lupus patients is hypomethylated, which results in overexpression of methylation-regulated genes, T-cell autoreactivity, and autoimmunity in vivo. Inducing an extracellular signal-regulated kinase (ERK) signaling defect in T cells using a transgenic mouse model resulted in reduced DNA methyltransferase 1 (DNMT1) expression, overexpression of methylation-sensitive genes, and anti-double-stranded DNA (anti-dsDNA) antibody production. ERK signaling is known to be defective in lupus T cells, and this defect is now explained by impaired T-cell protein kinase C (PKC) delta activation. Herein, we discuss how defective epigenetic regulation is involved in the pathogenesis of lupus, which includes both DNA methylation and histone modification changes.
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