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Toyofuku E, Takeshita K, Ohnishi H, Kiridoshi Y, Masuoka H, Kadowaki T, Nishikomori R, Nishimura K, Kobayashi C, Ebato T, Shigemura T, Inoue Y, Suda W, Hattori M, Morio T, Honda K, Kanegane H. Dysregulation of the Intestinal Microbiome in Patients With Haploinsufficiency of A20. Front Cell Infect Microbiol 2022; 11:787667. [PMID: 35155270 PMCID: PMC8834539 DOI: 10.3389/fcimb.2021.787667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Haploinsufficiency of A20 (HA20) is a form of inborn errors of immunity (IEI). IEIs are genetically occurring diseases, some of which cause intestinal dysbiosis. Due to the dysregulation of regulatory T cells (Tregs) observed in patients with HA20, gut dysbiosis was associated with Tregs in intestinal lamina propria. Methods Stool samples were obtained from 16 patients with HA20 and 15 of their family members. Infant samples and/or samples with recent antibiotics use were excluded; hence, 26 samples from 13 patients and 13 family members were analyzed. The 16S sequencing process was conducted to assess the microbial composition of samples. Combined with clinical information, the relationship between the microbiome and the disease activity was statistically analyzed. Results The composition of gut microbiota in patients with HA20 was disturbed compared with that in healthy family members. Age, disease severity, and use of immunosuppressants corresponded to dysbiosis. However, other explanatory factors, such as abdominal symptoms and probiotic treatment, were not associated. The overall composition at the phylum level was stable, but some genera were significantly increased or decreased. Furthermore, among the seven operational taxonomic units (OTUs) that increased, two OTUs, Streptococcus mutans and Lactobacillus salivarius, considerably increased in patients with autoantibodies than those without autoantibodies. Discussion Detailed interaction on intestinal epithelium remains unknown; the relationship between the disease and stool composition change helps us understand the mechanism of an immunological reaction to microorganisms.
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Affiliation(s)
- Etsushi Toyofuku
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kozue Takeshita
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yuko Kiridoshi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corporation, Tokyo, Japan
| | - Hiroaki Masuoka
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomonori Kadowaki
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ryuta Nishikomori
- Department of Pediatrics, Kyoto University Hospital, Kyoto, Japan
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Kenichi Nishimura
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chie Kobayashi
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takasuke Ebato
- Department of Pediatrics, Kitasato University Hospital, Sagamihara, Japan
| | - Tomonari Shigemura
- Department of Pediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yuzaburo Inoue
- Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kenya Honda
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Zou M, Zeng QS, Nie J, Yang JH, Luo ZY, Gan HT. The Role of E3 Ubiquitin Ligases and Deubiquitinases in Inflammatory Bowel Disease: Friend or Foe? Front Immunol 2021; 12:769167. [PMID: 34956195 PMCID: PMC8692584 DOI: 10.3389/fimmu.2021.769167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/17/2021] [Indexed: 02/05/2023] Open
Abstract
Inflammatory bowel disease (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), exhibits a complex multifactorial pathogenesis involving genetic susceptibility, imbalance of gut microbiota, mucosal immune disorder and environmental factors. Recent studies reported associations between ubiquitination and deubiquitination and the occurrence and development of inflammatory bowel disease. Ubiquitination modification, one of the most important types of post-translational modifications, is a multi-step enzymatic process involved in the regulation of various physiological processes of cells, including cell cycle progression, cell differentiation, apoptosis, and innate and adaptive immune responses. Alterations in ubiquitination and deubiquitination can lead to various diseases, including IBD. Here, we review the role of E3 ubiquitin ligases and deubiquitinases (DUBs) and their mediated ubiquitination and deubiquitination modifications in the pathogenesis of IBD. We highlight the importance of this type of posttranslational modification in the development of inflammation, and provide guidance for the future development of targeted therapeutics in IBD.
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Affiliation(s)
- Min Zou
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Qi-Shan Zeng
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Nie
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Jia-Hui Yang
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen-Yi Luo
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Hua-Tian Gan
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
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Abstract
Inflammation is triggered by stimulation of innate sensors that recognize pathogens, chemical and physical irritants, and damaged cells subsequently initiating a well-orchestrated adaptive immune response. Immune cell activation is a strictly regulated and self-resolving process supported by an array of negative feedback mechanisms to sustain tissue homeostasis. The disruption of these regulatory pathways forms the basis of chronic inflammatory diseases, including periodontitis. Ubiquitination, a covalent posttranslational modification of target proteins with ubiquitin, has a profound effect on the stability and activity of its substrates, thereby regulating the immune system at molecular and cellular levels. Through the cooperative actions of E3 ubiquitin ligases and deubiquitinases, ubiquitin modifications are implicated in several biological processes, including proteasomal degradation, transcriptional regulation, regulation of protein-protein interactions, endocytosis, autophagy, DNA repair, and cell cycle regulation. A20 (tumor necrosis factor α-induced protein 3 or TNFAIP3) is a ubiquitin-editing enzyme that mainly functions as an endogenous regulator of inflammation through termination of nuclear factor (NF)-κB activation as part of a negative feedback loop. A20 interacts with substrates that reside downstream of immune sensors, including Toll-like receptors, nucleotide-binding oligomerization domain-containing receptors, lymphocyte receptors, and cytokine receptors. Due to its pleiotropic functions as a ubiquitin binding protein, deubiquitinase and ubiquitin ligase, and its versatile role in various signaling pathways, aberrant A20 levels are associated with numerous conditions such as rheumatoid arthritis, diabetes, systemic lupus erythematosus, inflammatory bowel disease, psoriasis, Sjögren syndrome, coronary artery disease, multiple sclerosis, cystic fibrosis, asthma, cancer, neurological disorders, and aging-related sequelae. Similarly, A20 has recently been implicated as an essential regulator of inflammation in the oral cavity. This review presents information on the ubiquitin system and regulation of NF-κB by ubiquitination using A20 as a representative molecule and highlights how the dysregulation of this system can lead to several immune pathologies, including oral cavity-related disorders mainly focusing on periodontitis.
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Affiliation(s)
- E.C. Mooney
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Philips Institute for Oral Health Research, Virginia Commonwealth University, School of Dentistry, Richmond, VA, USA
| | - S.E. Sahingur
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Razani B, Malynn BA, Ma A. Preserving immune homeostasis with A20. Adv Immunol 2020; 148:1-48. [PMID: 33190732 DOI: 10.1016/bs.ai.2020.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A20/TNFAIP3 is a TNF induced gene that plays a profound role in preserving cellular and organismal homeostasis (Lee, et al., 2000; Opipari etal., 1990). This protein has been linked to multiple human diseases via genetic, epigenetic, and an emerging series of patients with mono-allelic coding mutations. Diverse cellular functions of this pleiotropically expressed protein include immune-suppressive, anti-inflammatory, and cell protective functions. The A20 protein regulates ubiquitin dependent cell signals; however, the biochemical mechanisms by which it performs these functions is surprisingly complex. Deciphering these cellular and biochemical facets of A20 dependent biology should greatly improve our understanding of murine and human disease pathophysiology as well as unveil new mechanisms of cell and tissue biology.
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Affiliation(s)
- Bahram Razani
- Department of Dermatology, University of California, San Francisco, CA, United States
| | - Barbara A Malynn
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Averil Ma
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States.
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Rees WD, Sly LM, Steiner TS. How do immune and mesenchymal cells influence the intestinal epithelial cell compartment in inflammatory bowel disease? Let's crosstalk about it! J Leukoc Biol 2020; 108:309-321. [PMID: 32057139 DOI: 10.1002/jlb.3mir0120-567r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/12/2020] [Accepted: 01/17/2020] [Indexed: 12/18/2022] Open
Abstract
Intestinal epithelial cells provide a front line of defense by establishing a barrier against food Ags, pathogens, and commensal microorganisms. This defense includes the establishment of a tolerogenic environment in the gastrointestinal (GI) tract. The intestinal epithelium replenishes itself by cell turnover every 4-5 days, and this process is facilitated by various pathways of communication between the intestinal epithelial cells (IECs), the underlying stromal cell network, and professional immune cells, which together help establish a proper intestinal stem cell (ISC) niche in the crypt. However, during a state of inflammation, such as in inflammatory bowel diseases (IBD), these communication pathways can be altered, and this can lead to the development of inflammatory IECs within the crypt that further drive inflammation. Here, we review the current literature looking at crosstalk between immune cells, stromal cells, and IECs: how does the immune system potentially alter the ISC niche, and how do IECs influence intestinal immunity? We discuss the latest research using single cell RNA sequencing and intestinal organoid cultures to help answer these questions. A better understanding of this complex crosstalk can help lead to a better understanding of intestinal biology in general, and more efficient therapeutic approaches to treat IBD.
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Affiliation(s)
- William D Rees
- Department of Medicine, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laura M Sly
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Theodore S Steiner
- Department of Medicine, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Papa R, Picco P, Gattorno M. The expanding pathways of autoinflammation: a lesson from the first 100 genes related to autoinflammatory manifestations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 120:1-44. [PMID: 32085880 DOI: 10.1016/bs.apcsb.2019.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AutoInflammatory Diseases (AIDs) are a group of innate immune system disorders characterized by sterile inflammation without evidence of pathogenic autoantibodies or auto-reactive T lymphocytes. An expanding spectrum of genes and molecular pathways are associated with AIDs. Inflammasomopathies are secondary to dysregulation of multi-protein complexes, called inflammasomes, leading to an excessive maturation and secretion of IL1β and IL18. Patients present with persistent or recurrent systemic inflammation, abdominal and chest pain, skin rashes and are sensible to IL1 inhibitors. Unfolded proteins response causes a small number of AIDs that we propose to call immuno-proteinopathies, characterized by recurrent fevers and deep tissues inflammation. Other inflammatory conditions can occur in case of abnormalities of actin polymerization and the term of immuno-actinopathies is proposed. Generalized pustular psoriasis is a marker of autoinflammation mainly affecting the keratinocytes. Specific treatment targeting the p40 subunit of IL12 and IL23 or IL-17 are usually effective. Granulomatous inflammation characterizes AIDs related to NOD2 signaling defects. Defects in the ubiquitin-proteasome system cause a group of relopathies and some interferonopathies related to defect of the proteasome function (CANDLE syndrome). Gain of function of proteins regulating the production of type I interferons lead to severe inflammatory conditions, called interferonopathies. The JAK/STAT inhibitors are usually effective in these latter conditions. In conclusions, the identification of the main intracellular pathways involved in rare monogenic AIDs allows not only the proper classification of different conditions, but also highlight a pivotal role of possible novel therapeutic targets for the future.
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Affiliation(s)
- Riccardo Papa
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
| | - Paolo Picco
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
| | - Marco Gattorno
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
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