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Lin Z, Chen Q, Ruan HB. To die or not to die: Gasdermins in intestinal health and disease. Semin Immunol 2024; 71:101865. [PMID: 38232665 PMCID: PMC10872225 DOI: 10.1016/j.smim.2024.101865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024]
Abstract
Intestinal homeostasis is achieved by the balance among intestinal epithelium, immune cells, and gut microbiota. Gasdermins (GSDMs), a family of membrane pore forming proteins, can trigger rapid inflammatory cell death in the gut, mainly pyroptosis and NETosis. Importantly, there is increasing literature on the non-cell lytic roles of GSDMs in intestinal homeostasis and disease. While GSDMA is low and PJVK is not expressed in the gut, high GSDMB and GSDMC expression is found almost restrictively in intestinal epithelial cells. Conversely, GSDMD and GSDME show more ubiquitous expression among various cell types in the gut. The N-terminal region of GSDMs can be liberated for pore formation by an array of proteases in response to pathogen- and danger-associated signals, but it is not fully understood what cell type-specific mechanisms activate intestinal GSDMs. The host relies on GSDMs for pathogen defense, tissue tolerance, and cancerous cell death; however, pro-inflammatory milieu caused by pyroptosis and excessive cytokine release may favor the development and progression of inflammatory bowel disease and cancer. Therefore, a thorough understanding of spatiotemporal mechanisms that control gasdermin expression, activation, and function is essential for the development of future therapeutics for intestinal disorders.
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Affiliation(s)
- Zhaoyu Lin
- MOE Key Laboratory of Model Animals for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Qianyue Chen
- MOE Key Laboratory of Model Animals for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, National Resource Center for Mutant Mice of China, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Hai-Bin Ruan
- Department of Integrative Biology and Physiology, University of Minnesota Medical School, Minneapolis, MN, USA; Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.
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2
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Slaufova M, Karakaya T, Di Filippo M, Hennig P, Beer HD. The gasdermins: a pore-forming protein family expressed in the epidermis. Front Immunol 2023; 14:1254150. [PMID: 37771587 PMCID: PMC10523161 DOI: 10.3389/fimmu.2023.1254150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Gasdermins comprise a family of pore-forming proteins, which play critical roles in (auto)inflammatory diseases and cancer. They are expressed as self-inhibited precursor proteins consisting of an aminoterminal cytotoxic effector domain (NT-GSDM) and a carboxyterminal inhibitor domain (GSDM-CT) separated by an unstructured linker region. Proteolytic processing in the linker region liberates NT-GSDM, which translocates to membranes, forms oligomers, and induces membrane permeabilization, which can disturb the cellular equilibrium that can lead to cell death. Gasdermin activation and pore formation are associated with inflammation, particularly when induced by the inflammatory protease caspase-1 upon inflammasome activation. These gasdermin pores allow the release of the pro-inflammatory cytokines interleukin(IL)-1β and IL-18 and induce a lytic type of cell death, termed pyroptosis that supports inflammation, immunity, and tissue repair. However, even at the cellular level, the consequences of gasdermin activation are diverse and range from induction of programmed cell death - pyroptosis or apoptosis - to poorly characterized protective mechanisms. The specific effects of gasdermin activation can vary between species, cell types, the membrane that is being permeabilized (plasma membrane, mitochondrial membrane, etc.), and the overall biological state of the local tissue/cells. In epithelia, gasdermins seem to play crucial roles. Keratinocytes represent the main cell type of the epidermis, which is the outermost skin layer with an essential barrier function. Compared to other tissues, keratinocytes express all members of the gasdermin family, in part in a differentiation-specific manner. That raises questions regarding the specific roles of individual GSDM family members in the skin, the mechanisms and consequences of their activation, and the potential crosstalk between them. In this review, we summarize the current knowledge about gasdermins with a focus on keratinocytes and the skin and discuss the possible roles of the different family members in immunity and disease.
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Affiliation(s)
- Marta Slaufova
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Tugay Karakaya
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Michela Di Filippo
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Paulina Hennig
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Hans-Dietmar Beer
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
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Liu Y, Lei H, Zhang W, Xing Q, Liu R, Wu S, Liu Z, Yan Q, Li W, Liu X, Hu Y. Pyroptosis in renal inflammation and fibrosis: current knowledge and clinical significance. Cell Death Dis 2023; 14:472. [PMID: 37500614 PMCID: PMC10374588 DOI: 10.1038/s41419-023-06005-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Pyroptosis is a novel inflammatory form of regulated cell death (RCD), characterized by cell swelling, membrane rupture, and pro-inflammatory effects. It is recognized as a potent inflammatory response required for maintaining organismal homeostasis. However, excessive and persistent pyroptosis contributes to severe inflammatory responses and accelerates the progression of numerous inflammation-related disorders. In pyroptosis, activated inflammasomes cleave gasdermins (GSDMs) and generate membrane holes, releasing interleukin (IL)-1β/18, ultimately causing pyroptotic cell death. Mechanistically, pyroptosis is categorized into caspase-1-mediated classical pyroptotic pathway and caspase-4/5/11-mediated non-classical pyroptotic pathway. Renal fibrosis is a kidney disease characterized by the loss of structural and functional units, the proliferation of fibroblasts and myofibroblasts, and extracellular matrix (ECM) accumulation, which leads to interstitial fibrosis of the kidney tubules. Histologically, renal fibrosis is the terminal stage of chronic inflammatory kidney disease. Although there is a multitude of newly discovered information regarding pyroptosis, the regulatory roles of pyroptosis involved in renal fibrosis still need to be fully comprehended, and how to improve clinical outcomes remains obscure. Hence, this review systematically summarizes the novel findings regarding the role of pyroptosis in the pathogenesis of renal fibrosis and discusses potential biomarkers and drugs for anti-fibrotic therapeutic strategies.
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Affiliation(s)
- Ya Liu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Haibo Lei
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Wenyou Zhang
- Department of Pharmacy, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Qichang Xing
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Renzhu Liu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Shiwei Wu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Zheng Liu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Qingzi Yan
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Wencan Li
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China
| | - Xiang Liu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China.
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China.
| | - Yixiang Hu
- Molecular Pharmacology Laboratory, Department of Clinical Pharmacy, Xiangtan Center Hospital, Xiangtan, 411100, China.
- Honghao Zhou Research Institute, Xiangtan Center Hospital, Xiangtan, 411100, China.
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Song Q, Mao X, Jing M, Fu Y, Yan W. Pathophysiological role of BACH transcription factors in digestive system diseases. Front Physiol 2023; 14:1121353. [PMID: 37228820 PMCID: PMC10203417 DOI: 10.3389/fphys.2023.1121353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
BTB and CNC homologous (BACH) proteins, including BACH1 and BACH2, are transcription factors that are widely expressed in human tissues. BACH proteins form heterodimers with small musculoaponeurotic fibrosarcoma (MAF) proteins to suppress the transcription of target genes. Furthermore, BACH1 promotes the transcription of target genes. BACH proteins regulate physiological processes, such as the differentiation of B cells and T cells, mitochondrial function, and heme homeostasis as well as pathogenesis related to inflammation, oxidative-stress damage caused by drugs, toxicants, or infections; autoimmunity disorders; and cancer angiogenesis, epithelial-mesenchymal transition, chemotherapy resistance, progression, and metabolism. In this review, we discuss the function of BACH proteins in the digestive system, including the liver, gallbladder, esophagus, stomach, small and large intestines, and pancreas. BACH proteins directly target genes or indirectly regulate downstream molecules to promote or inhibit biological phenomena such as inflammation, tumor angiogenesis, and epithelial-mesenchymal transition. BACH proteins are also regulated by proteins, miRNAs, LncRNAs, labile iron, and positive and negative feedback. Additionally, we summarize a list of regulators targeting these proteins. Our review provides a reference for future studies on targeted drugs in digestive diseases.
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Affiliation(s)
- Qianben Song
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Mao
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengjia Jing
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu Fu
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Liver and Gastrointestinal Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Li S, Bracey S, Liu Z, Xiao TS. Regulation of gasdermins in pyroptosis and cytokine release. Adv Immunol 2023; 158:75-106. [PMID: 37453754 PMCID: PMC10874695 DOI: 10.1016/bs.ai.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Gasdermins are effectors of pyroptosis downstream of diverse signaling pathways. Emerging evidence suggests that a number of post-translational modifications regulate the function of gasdermins in pyroptosis, a highly inflammatory form of cell death, and lytic or non-lytic secretion of intracellular contents. These include processing by different caspases and other proteases that may activate or suppress pyroptosis, ubiquitination by a bacterial E3 ligase that suppresses pyroptosis as an immune evasion mechanism, modifications at Cys residues in mammalian or microbial gasdermins that promote or inhibit pyroptosis, and potential phosphorylation that represses pyroptosis. Such diverse regulatory mechanisms by host and microbial proteases, ubiquitin ligases, acyltransferases, kinases and phosphatases may underlie the divergent physiological and pathological functions of gasdermins, and furnish opportunities for therapeutic targeting of gasdermins in infectious diseases and inflammatory disorders.
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Affiliation(s)
- Sai Li
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Syrena Bracey
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Zhonghua Liu
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States.
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States.
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Ivanov AI, Rana N, Privitera G, Pizarro TT. The enigmatic roles of epithelial gasdermin B: Recent discoveries and controversies. Trends Cell Biol 2023; 33:48-59. [PMID: 35821185 PMCID: PMC9789163 DOI: 10.1016/j.tcb.2022.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 01/06/2023]
Abstract
Gasdermin B (GSDMB) belongs to a family of structurally related proteins [(i.e., gasdermins (GSDMs)]. It distinguishes itself from other members by the lack of autoinhibition but clear bioactivity of its full-length form, its preference to bind to phosphatidylinositol phosphates and sulfatides, and the ability to promote both lytic and nonlytic cellular functions. It is the only gasdermin that lacks a mouse ortholog, making in vivo mechanistic studies challenging to perform. GSDMB is abundantly expressed in epithelial cells lining organs that directly interface with the external environment, such as the gastrointestinal tract, with emerging evidence supporting its role in enteric infections, inflammatory bowel disease (IBD), and colorectal cancer. This review discusses the unique features of GSDMB among other gasdermin family members and controversies surrounding GSDMB-dependent mammalian inflammatory cell death (i.e., pyroptosis), including recent discoveries revealing both lytic and nonlytic functions of epithelial-derived GSDMB, particularly during gut health and disease.
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Affiliation(s)
- Andrei I Ivanov
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Nitish Rana
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Giuseppe Privitera
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Theresa T Pizarro
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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Ghiboub M, Koster J, Craggs PD, Li Yim AYF, Shillings A, Hutchinson S, Bingham RP, Gatfield K, Hageman IL, Yao G, O’Keefe HP, Coffin A, Patel A, Sloan LA, Mitchell DJ, Hayhow TG, Lunven L, Watson RJ, Blunt CE, Harrison LA, Bruton G, Kumar U, Hamer N, Spaull JR, Zwijnenburg DA, Welting O, Hakvoort TBM, te Velde AA, van Limbergen J, Henneman P, Prinjha RK, de Winther MPJ, Harker NR, Tough DF, de Jonge WJ. Modulation of macrophage inflammatory function through selective inhibition of the epigenetic reader protein SP140. BMC Biol 2022; 20:182. [PMID: 35986286 PMCID: PMC9392322 DOI: 10.1186/s12915-022-01380-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 07/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background SP140 is a bromodomain-containing protein expressed predominantly in immune cells. Genetic polymorphisms and epigenetic modifications in the SP140 locus have been linked to Crohn’s disease (CD), suggesting a role in inflammation. Results We report the development of the first small molecule SP140 inhibitor (GSK761) and utilize this to elucidate SP140 function in macrophages. We show that SP140 is highly expressed in CD mucosal macrophages and in in vitro-generated inflammatory macrophages. SP140 inhibition through GSK761 reduced monocyte-to-inflammatory macrophage differentiation and lipopolysaccharide (LPS)-induced inflammatory activation, while inducing the generation of CD206+ regulatory macrophages that were shown to associate with a therapeutic response to anti-TNF in CD patients. SP140 preferentially occupies transcriptional start sites in inflammatory macrophages, with enrichment at gene loci encoding pro-inflammatory cytokines/chemokines and inflammatory pathways. GSK761 specifically reduces SP140 chromatin binding and thereby expression of SP140-regulated genes. GSK761 inhibits the expression of cytokines, including TNF, by CD14+ macrophages isolated from CD intestinal mucosa. Conclusions This study identifies SP140 as a druggable epigenetic therapeutic target for CD. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01380-6.
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Magnani L, Colantuoni M, Mortellaro A. Gasdermins: New Therapeutic Targets in Host Defense, Inflammatory Diseases, and Cancer. Front Immunol 2022; 13:898298. [PMID: 35844522 PMCID: PMC9285118 DOI: 10.3389/fimmu.2022.898298] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Gasdermins (GSDMs) are a class of pore-forming proteins related to pyroptosis, a programmed cell death pathway that is induced by a range of inflammatory stimuli. Small-scale GSDM activation and pore formation allow the passive release of cytokines, such as IL-1β and IL-18, and alarmins, but, whenever numerous GSDM pores are assembled, osmotic lysis and cell death occur. Such GSDM-mediated pyroptosis promotes pathogen clearance and can help restore homeostasis, but recent studies have revealed that dysregulated pyroptosis is at the root of many inflammation-mediated disease conditions. Moreover, new homeostatic functions for gasdermins are beginning to be revealed. Here, we review the newly discovered mechanisms of GSDM activation and their prominent roles in host defense and human diseases associated with chronic inflammation. We also highlight the potential of targeting GSDMs as a new therapeutic approach to combat chronic inflammatory diseases and cancer and how we might overcome the current obstacles to realize this potential.
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Abell NS, DeGorter MK, Gloudemans MJ, Greenwald E, Smith KS, He Z, Montgomery SB. Multiple causal variants underlie genetic associations in humans. Science 2022; 375:1247-1254. [PMID: 35298243 DOI: 10.1126/science.abj5117] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Associations between genetic variation and traits are often in noncoding regions with strong linkage disequilibrium (LD), where a single causal variant is assumed to underlie the association. We applied a massively parallel reporter assay (MPRA) to functionally evaluate genetic variants in high, local LD for independent cis-expression quantitative trait loci (eQTL). We found that 17.7% of eQTLs exhibit more than one major allelic effect in tight LD. The detected regulatory variants were highly and specifically enriched for activating chromatin structures and allelic transcription factor binding. Integration of MPRA profiles with eQTL/complex trait colocalizations across 114 human traits and diseases identified causal variant sets demonstrating how genetic association signals can manifest through multiple, tightly linked causal variants.
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Affiliation(s)
- Nathan S Abell
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Marianne K DeGorter
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Emily Greenwald
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA.,Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA.,Department of Pathology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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Sasahara Y, Uchida T, Suzuki T, Abukawa D. Primary Immunodeficiencies Associated With Early-Onset Inflammatory Bowel Disease in Southeast and East Asia. Front Immunol 2022; 12:786538. [PMID: 35095863 PMCID: PMC8792847 DOI: 10.3389/fimmu.2021.786538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/21/2021] [Indexed: 12/02/2022] Open
Abstract
Background Causes of early-onset inflammatory bowel disease (IBD) vary, and primary immunodeficiency diseases (PIDs) are associated with early-onset IBD as monogenic disorders. Aim This review investigates the prevalence, clinical manifestation, genetic profile, and treatment of patients with early-onset IBD in Southeast and East Asia. Methods A systemic review of articles reporting PID patients associated with early-onset IBD in Southeast and East Asia was conducted. Results The prevalence of PID associated with IBD was higher than that reported in western nations, and the frequency of patients with bloody stools as an early symptom was relatively higher in monogenic diseases. A total 13 (12.0%) of 108 patients with early-onset IBD were diagnosed as PID by exome sequencing and targeted gene panel analysis in Japan, including four patients with XIAP, three with IL10RA, and two or one patient with other gene mutations. In addition, ten patients were reported as having IL-10 receptor alpha (IL-10RA) deficiency in China and Hong Kong. Allogeneic hematopoietic stem cell transplantation was performed in patients with X-linked inhibitor of apoptosis deficiency, IL-10RA deficiency, or other PID as a curative treatment, and the preferable outcome of reduced-intensity conditioning and complete resolution of IBD symptoms and dysbiosis were achieved. Conclusion Comprehensive molecular diagnosis has been widely applied to screen for patients with PID-associated IBD in Southeast and East Asia. These results contributed to the awareness of monogenic PID in early-onset IBD patients and their differences in clinical manifestations and genetic profiles compared to the patients in western counties.
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Affiliation(s)
- Yoji Sasahara
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Uchida
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tasuku Suzuki
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daiki Abukawa
- Department of General Pediatrics, Gastroenterology and Hepatology, Miyagi Children's Hospital, Sendai, Japan
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Molecular and structural aspects of gasdermin family pores and insights into gasdermin-elicited programmed cell death. Biochem Soc Trans 2021; 49:2697-2710. [PMID: 34812891 PMCID: PMC8786298 DOI: 10.1042/bst20210672] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
Pyroptosis is a highly inflammatory and lytic type of programmed cell death (PCD) commenced by inflammasomes, which sense perturbations in the cytosolic environment. Recently, several ground-breaking studies have linked a family of pore-forming proteins known as gasdermins (GSDMs) to pyroptosis. The human genome encodes six GSDM proteins which have a characteristic feature of forming pores in the plasma membrane resulting in the disruption of cellular homeostasis and subsequent induction of cell death. GSDMs have an N-terminal cytotoxic domain and an auto-inhibitory C-terminal domain linked together through a flexible hinge region whose proteolytic cleavage by various enzymes releases the N-terminal fragment that can insert itself into the inner leaflet of the plasma membrane by binding to acidic lipids leading to pore formation. Emerging studies have disclosed the involvement of GSDMs in various modalities of PCD highlighting their role in diverse cellular and pathological processes. Recently, the cryo-EM structures of the GSDMA3 and GSDMD pores were resolved which have provided valuable insights into the pore formation process of GSDMs. Here, we discuss the current knowledge regarding the role of GSDMs in PCD, structural and molecular aspects of autoinhibition, and pore formation mechanism followed by a summary of functional consequences of gasdermin-induced membrane permeabilization.
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12
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Du T, Gao J, Li P, Wang Y, Qi Q, Liu X, Li J, Wang C, Du L. Pyroptosis, metabolism, and tumor immune microenvironment. Clin Transl Med 2021; 11:e492. [PMID: 34459122 PMCID: PMC8329701 DOI: 10.1002/ctm2.492] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
In response to a wide range of stimulations, host cells activate pyroptosis, a kind of inflammatory cell death which is provoked by the cytosolic sensing of danger signals and pathogen infection. In manipulating the cleavage of gasdermins (GSDMs), researchers have found that GSDM proteins serve as the real executors and the deterministic players in fate decisions of pyroptotic cells. Whether inflammatory characteristics induced by pyroptosis could cause damage the host or improve immune activity is largely dependent on the context, timing, and response degree. Here, we systematically review current points involved in regulatory mechanisms and the multidimensional roles of pyroptosis in several metabolic diseases and the tumor microenvironment. Targeting pyroptosis may reveal potential therapeutic avenues.
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Affiliation(s)
- Tiantian Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Jie Gao
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Peilong Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Yunshan Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Qiuchen Qi
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Xiaoyan Liu
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Juan Li
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
| | - Chuanxin Wang
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
| | - Lutao Du
- Department of Clinical LaboratoryThe Second HospitalCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Engineering and Technology Research Center for Tumor Marker DetectionJinanShandongChina
- Shandong Provincial Clinical Medicine Research Center for Clinical LaboratoryJinanShandongChina
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Di Narzo AF, Hart A, Kosoy R, Peters L, Stojmirovic A, Cheng H, Zhang Z, Shan M, Cho J, Kasarskis A, Argmann C, Peter I, Schadt EE, Hao K. Polygenic risk score for alcohol drinking behavior improves prediction of inflammatory bowel disease risk. Hum Mol Genet 2021; 30:514-523. [PMID: 33601420 PMCID: PMC8599895 DOI: 10.1093/hmg/ddab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/23/2021] [Accepted: 02/03/2021] [Indexed: 02/05/2023] Open
Abstract
Epidemiological studies have long recognized risky behaviors as potentially modifiable factors for the onset and flares of inflammatory bowel disease (IBD); yet, the underlying mechanisms are largely unknown. Recently, the genetic susceptibilities to cigarette smoking, alcohol and cannabis use [i.e. substance use (SU)] have been characterized by well-powered genome-wide association studies (GWASs). We aimed to assess the impact of genetic determinants of SU on IBD risk. Using Mount Sinai Crohn's and Colitis Registry (MSCCR) cohort of 1058 IBD cases and 188 healthy controls, we computed the polygenic risk score (PRS) for SU and correlated them with the observed IBD diagnoses, while adjusting for genetic ancestry, PRS for IBD and SU behavior at enrollment. The results were validated in a pediatric cohort with no SU exposure. PRS of alcohol consumption (DrnkWk), smoking cessation and age of smoking initiation, were associated with IBD risk in MSCCR even after adjustment for PRSIBD and actual smoking status. One interquartile range decrease in PRSDrnkWk was significantly associated to higher IBD risk (i.e. inverse association) (with odds ratio = 1.65 and 95% confidence interval: 1.32, 2.06). The association was replicated in a pediatric Crohn's disease cohort. Colocalization analysis identified a locus on chromosome 16 with polymorphisms in IL27, SULT1A2 and SH2B1, which reached genome-wide statistical significance in GWAS (P < 7.7e-9) for both alcohol consumption and IBD risk. This study demonstrated that the genetic predisposition to SU was associated with IBD risk, independent of PRSIBD and in the absence of SU behaviors. Our study may help further stratify individuals at risk of IBD.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amy Hart
- Immunology Translational Sciences, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | | | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mingxu Shan
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
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14
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Tang Z, Zhang P, Ji M, Yin C, Zhao R, Huang Z, Huang Y. Characterization of novel and large fragment deletions in exon 1 of the IL10RA gene in Chinese children with very early onset inflammatory bowel diseases. BMC Gastroenterol 2021; 21:167. [PMID: 33849446 PMCID: PMC8045347 DOI: 10.1186/s12876-021-01756-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/08/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Defects in interleukin 10 (IL10) and its receptors are particularly involved in very early onset inflammatory bowel disease (VEOIBD). However, large fragment deletions of IL10 receptor A (IL10RA) are rare. METHODS VEOIBD patients with confirmed mutations in the IL10RA gene were enrolled from January 1, 2019 to June 30, 2020. The clinical features and endoscopic-radiological findings of the patients with large fragment deletions of the IL10RA gene were determined and followed up. RESULTS Thirty-five patients with IL10RA gene mutations, namely, 28 compound heterozygous mutations and 7 homozygote mutations, were enrolled in this study. Six patients carried the reported point mutation c.301C > T (p. R101RW) or c.537 G > A (p. T179T) in one locus and a large fragment deletion in exon 1 in another locus, which were novel mutations in this gene. A 333-bp deletion of exon 1 (117857034-11857366 del) was the main mutation in this locus in 85.7% of the patients with large fragment deletions. The time of disease onset ranged from birth to 4 years, and diarrhea was the main initial symptom. In total, 6/7 patients had perianal complications, including perianal abscess, fistula and skin tags. Six patients accepted thalidomide treatment, 5/7 accepted mesalamine, 3/7 accepted hematopoietic stem cell transplantation (HSCT), and 3/7 were waiting for HSCT. CONCLUSIONS We identified a novel large deletion of exon 1 involving the IL10RA gene for the first time and showed the characteristics of VEOIBD patients. This study expands the spectrum of Chinese VEOIBD patients with IL0RA gene mutations.
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Affiliation(s)
- Zifei Tang
- Department of Gastroenterology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, 201102, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Min Ji
- Department of Radiology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Chunlan Yin
- Department of Gastroenterology, Children's Hospital of Hebei Province, Shijiazhuang, 050030, China
| | - Ruiqin Zhao
- Department of Gastroenterology, Children's Hospital of Hebei Province, Shijiazhuang, 050030, China
| | - Zhiheng Huang
- Department of Gastroenterology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, 201102, China.
| | - Ying Huang
- Department of Gastroenterology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, 201102, China.
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15
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Zihlif M, Mahafza T, Froukh T, Al-Akhras FM, Alsalman R, Zuriekat M, Naffa R. Association between Gasdermin A, Gasdermin B Polymorphisms and Allergic Rhinitis Amongst Jordanians. Endocr Metab Immune Disord Drug Targets 2021; 21:472-477. [PMID: 32496997 DOI: 10.2174/1871530320666200604161656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Gasdermin A (GSDMA) and Gasdermin B (GSDMB) have been associated with childhood and to a lesser extent with adult asthma in many populations. In this study, we investigate whether there is an association between GSDMA (rs7212938, T/G) and GSDMB (rs7216389, T/C) at locus 17q21.2 and risk of Allergic Rhinitis among Jordanians. Also, we aimed to determine if there is an association between such polymorphisms and the IgE level. METHODS The study included 112 rhinitis patients and 111 Healthy controls. Gasdermin A (GSDMA) (rs7212938, T/G) and Gasdermin B (rs7216389, T/C) polymorphisms were genotyped using the PCRRFLP method. RESULTS On the genotype level, three analysis models were applied namely co-dominant, dominant and recessive genotypes. GSDMB CC genotype was found to have a significant protective effect against allergic Rhinitis (< 0.05). cc genotype was also significantly associated with higher IgE level among the studied population. CONCLUSION The GSDMB CC of homozygous minor genotype showed a protective effect against Allergic rhinitis. It also was found to be significantly associated with lower IgE level among the studied population. No association was found between GSDMA with the risk of allergic Rhinitis.
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Affiliation(s)
- Malek Zihlif
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman, Jordan
| | - Tareq Mahafza
- Department of Special Surgery, University of Jordan Hospital, The University of Jordan, Amman, Jordan
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Faculty of Science, Philadelphia University, Amman, Jordan
| | - Fatima M Al-Akhras
- Department of Physiology and Biochemistry, Faculty of Medicine, The University of Jordan, Amman, Jordan
| | - Rami Alsalman
- Department of Special Surgery, University of Jordan Hospital, The University of Jordan, Amman, Jordan
| | - Margaret Zuriekat
- Department of Special Surgery, University of Jordan Hospital, The University of Jordan, Amman, Jordan
| | - Randa Naffa
- Department of Physiology and Biochemistry, Faculty of Medicine, The University of Jordan, Amman, Jordan
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16
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Nakamura A, Boroojeni SF, Haroon N. Aberrant antigen processing and presentation: Key pathogenic factors leading to immune activation in Ankylosing spondylitis. Semin Immunopathol 2021; 43:245-253. [PMID: 33532928 DOI: 10.1007/s00281-020-00833-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The strong association of HLA-B*27 with ankylosing spondylitis (AS) was first reported nearly 50 years ago. However, the mechanistic link between HLA-B*27 and AS has remained an enigma. While 85-90% of AS patients possess HLA-B*27, majority of HLA-B*27 healthy individuals do not develop AS. This suggests that additional genes and genetic regions interplay with HLA-B*27 to cause AS. Previous genome-wide association studies (GWAS) identified key genes that are distinctively expressed in AS, including the Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and ERAP2. As these gene-encoding molecules are primarily implicated in the process of peptide processing and presentation, potential pathological interaction of these molecules with HLA-B*27 may operate to cause AS by activating downstream immune responses. The aberrant peptide processing also gives rise to the accumulation of unstable protein complex in endoplasmic reticulum (ER), which drives endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) and activates autophagy. In this review, we describe the current hypotheses of AS pathogenesis, focusing on antigen processing and presentation operated by HLA-B*27 and associated molecules that may contribute to the disease initiation and progression of AS.
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Affiliation(s)
- Akihiro Nakamura
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Shaghayegh Foroozan Boroojeni
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Nigil Haroon
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada. .,Spondylitis Program, University Health Network, Toronto, Ontario, Canada. .,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada. .,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada. .,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada.
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17
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Tang L, Lu C, Zheng G, Burgering BM. Emerging insights on the role of gasdermins in infection and inflammatory diseases. Clin Transl Immunology 2020; 9:e1186. [PMID: 33033617 PMCID: PMC7533414 DOI: 10.1002/cti2.1186] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022] Open
Abstract
The gasdermins, family of pore-forming proteins, are emerging key regulators of infection, autoinflammation and antitumor immunity. Multiple studies have recently characterised their crucial roles in driving pyroptosis, a lytic pro-inflammatory type of cell death. Additionally, gasdermins also act as key effectors of NETosis, secondary necrosis and apoptosis. In this review, we will address current understanding of the mechanisms of gasdermin activation and further describe the protective and detrimental roles of gasdermins in host defence and autoinflammatory diseases. These data suggest that gasdermins play a prominent role in innate immunity and autoinflammatory disorders, thereby providing potential new therapeutic avenues for the treatment of infection and autoimmune disease.
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Affiliation(s)
- Lipeng Tang
- Department of Pharmacology of Traditional Chinese Medicine The Second Affiliated Hospital of Guangzhou University of Chinese Medicine Guangzhou China.,Department of Molecular Cancer Research Center Molecular Medicine University Medical Center Utrecht Utrecht The Netherlands
| | - Chuanjian Lu
- Department of Dermatology The Second Affiliated Hospital of Guangzhou University of Chinese Medicine Guangzhou China
| | - Guangjuan Zheng
- Department of Pharmacology of Traditional Chinese Medicine The Second Affiliated Hospital of Guangzhou University of Chinese Medicine Guangzhou China.,Department of Pathology The Second Affiliated Hospital of Guangzhou University of Chinese Medicine Guangzhou China
| | - Boudewijn Mt Burgering
- Department of Molecular Cancer Research Center Molecular Medicine University Medical Center Utrecht Utrecht The Netherlands
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18
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Kudelka MR, Stowell SR, Cummings RD, Neish AS. Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD. Nat Rev Gastroenterol Hepatol 2020; 17:597-617. [PMID: 32710014 PMCID: PMC8211394 DOI: 10.1038/s41575-020-0331-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel disease (IBD) affects 6.8 million people globally. A variety of factors have been implicated in IBD pathogenesis, including host genetics, immune dysregulation and gut microbiota alterations. Emerging evidence implicates intestinal epithelial glycosylation as an underappreciated process that interfaces with these three factors. IBD is associated with increased expression of truncated O-glycans as well as altered expression of terminal glycan structures. IBD genes, glycosyltransferase mislocalization, altered glycosyltransferase and glycosidase expression and dysbiosis drive changes in the glycome. These glycan changes disrupt the mucus layer, glycan-lectin interactions, host-microorganism interactions and mucosal immunity, and ultimately contribute to IBD pathogenesis. Epithelial glycans are especially critical in regulating the gut microbiota through providing bacterial ligands and nutrients and ultimately determining the spatial organization of the gut microbiota. In this Review, we discuss the regulation of intestinal epithelial glycosylation, altered epithelial glycosylation in IBD and mechanisms for how these alterations contribute to disease pathobiology. We hope that this Review provides a foundation for future studies on IBD glycosylation and the emergence of glycan-inspired therapies for IBD.
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Affiliation(s)
- Matthew R Kudelka
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA, USA
- Department of Internal Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sean R Stowell
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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19
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Transcription Factors That Regulate the Pathogenesis of Ulcerative Colitis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7402657. [PMID: 32908909 PMCID: PMC7468618 DOI: 10.1155/2020/7402657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/10/2020] [Indexed: 01/18/2023]
Abstract
Ulcerative colitis (UC) is one of the inflammatory bowel diseases (IBD) characterized by occurrence in the rectum and sigmoid colon of young adults. However, the functional roles of transcription factors (TFs) and their regulating target genes and pathways are not fully known in ulcerative colitis (UC). In this study, we collected gene expression data to identify differentially expressed TFs (DETFs). We found that differentially expressed genes (DEGs) were significantly enriched in the target genes of HOXA2, IKZF1, KLF2, XBP1, EGR2, ETV7, BACH2, CBFA2T3, HLF, and NFE2. TFs including BACH2, CBFA2T3, EGR2, ETV7, NFE2, and XBP1, and their target genes were significantly enriched in signaling by interleukins. BACH2 target genes were enriched in estrogen receptor- (ESR-) mediated signaling and nongenomic estrogen signaling. Furthermore, to clarify the functional roles of immune cells on the UC pathogenesis, we estimated the immune cell proportions in all the samples. The accumulated effector CD8 and reduced proportion of naïve CD4 might be responsible for the adaptive immune response in UC. The accumulation of plasma in UC might be associated with increased gut permeability. In summary, we present a systematic study of the TFs by analyzing the DETFs, their regulating target genes and pathways, and immune cells. These findings might improve our understanding of the TFs in the pathogenesis of UC.
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20
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Gruber C, Bogunovic D. Incomplete penetrance in primary immunodeficiency: a skeleton in the closet. Hum Genet 2020; 139:745-757. [PMID: 32067110 PMCID: PMC7275875 DOI: 10.1007/s00439-020-02131-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/02/2020] [Indexed: 12/11/2022]
Abstract
Primary immunodeficiencies (PIDs) comprise a diverse group of over 400 genetic disorders that result in clinically apparent immune dysfunction. Although PIDs are classically considered as Mendelian disorders with complete penetrance, we now understand that absent or partial clinical disease is often noted in individuals harboring disease-causing genotypes. Despite the frequency of incomplete penetrance in PID, no conceptual framework exists to categorize and explain these occurrences. Here, by reviewing decades of reports on incomplete penetrance in PID we identify four recurrent themes of incomplete penetrance, namely genotype quality, (epi)genetic modification, environmental influence, and mosaicism. For each of these principles, we review what is known, underscore what remains unknown, and propose future experimental approaches to fill the gaps in our understanding. Although the content herein relates specifically to inborn errors of immunity, the concepts are generalizable across genetic diseases.
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Affiliation(s)
- Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
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21
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Plichta DR, Graham DB, Subramanian S, Xavier RJ. Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships. Cell 2020; 178:1041-1056. [PMID: 31442399 DOI: 10.1016/j.cell.2019.07.045] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 07/25/2019] [Indexed: 02/08/2023]
Abstract
The current understanding of inflammatory bowel disease (IBD) pathogenesis implicates a complex interaction between host genetics, host immunity, microbiome, and environmental exposures. Mechanisms gleaned from genetics and molecular pathogenesis offer clues to the critical triggers of mucosal inflammation and guide the development of therapeutic interventions. A complex network of interactions between host genetic factors, microbes, and microbial metabolites governs intestinal homeostasis, making classification and mechanistic dissection of involved pathways challenging. In this Review, we discuss these challenges, areas of active translation, and opportunities for development of next-generation therapies.
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Affiliation(s)
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Sathish Subramanian
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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22
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Li L, Li Y, Bai Y. Role of GSDMB in Pyroptosis and Cancer. Cancer Manag Res 2020; 12:3033-3043. [PMID: 32431546 PMCID: PMC7201009 DOI: 10.2147/cmar.s246948] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/04/2020] [Indexed: 12/14/2022] Open
Abstract
Gasdermin B (GSDMB) belongs to the gasdermin (GSDM) family which may adopt different mechanisms of intramolecular domain interactions to modulate their lipid-binding and pore-forming activities. The GSDM family has regulatory functions in cell proliferation and differentiation, especially in pyroptosis process. Pyroptosis is a pro-inflammatory form of regulated cell death and is designed to attract a nonspecific innate response to the site of infection. For cancer cells, the activation of pyroptosis may promote cell death and exert anticancer properties. Also, recent studies have observed the pyroptosis-like features in GSDMB and some researches have shown that GSDMB overexpression occurred in several kinds of cancers; these findings bring a contradiction with the participation of GSDMB in pyroptosis. Although people pay less attention to GSDMB, it still has some essential research value. It is a paradox that GSDMB might participate in programmed cell death, which might put forward a research direction of therapeutic targets for cancer. Here, we review the possible progress of how GSDMB participated in this inflammatory regulation mechanistically and the potential functions of GSDMB in cancer.
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Affiliation(s)
- Lisha Li
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
| | - Yanjing Li
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
| | - Yuxian Bai
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, People's Republic of China
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23
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Lega S, Pin A, Arrigo S, Cifaldi C, Girardelli M, Bianco AM, Malamisura M, Angelino G, Faraci S, Rea F, Romeo EF, Aloi M, Romano C, Barabino A, Martelossi S, Tommasini A, Di Matteo G, Cancrini C, De Angelis P, Finocchi A, Bramuzzo M. Diagnostic Approach to Monogenic Inflammatory Bowel Disease in Clinical Practice: A Ten-Year Multicentric Experience. Inflamm Bowel Dis 2020; 26:720-727. [PMID: 31375816 DOI: 10.1093/ibd/izz178] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Multiple monogenic disorders present as very early onset inflammatory bowel disease (VEO-IBD) or as IBD with severe and atypical features. Establishing a genetic diagnosis may change patients' management and prognosis. In this study, we describe the diagnostic approach to suspected monogenic IBD in a real clinical setting, discussing genetic and phenotypic findings and therapeutic implications of molecular diagnosis. METHODS Information of patients with VEO-IBD and early onset IBD with severe/atypical phenotypes (EO-IBD s/a) managed between 2008-2017 who underwent a genetic workup were collected. RESULTS Ninety-three patients were included, and 12 (13%) reached a genetic diagnosis. Candidate sequencing (CS) was performed in 47 patients (50%), and next generation sequencing (NGS) was performed in 84 patients (90%). Candidate sequencing had a good diagnostic performance only when guided by clinical features specific for known monogenic diseases, whereas NGS helped finding new causative genetic variants and would have anticipated one monogenic diagnosis (XIAP) and consequent bone marrow transplant (BMT). Patients with monogenic IBD more frequently were male (92% vs 54%; P = 0.02), had extraintestinal findings (100% vs 34%; P < 0.001), and had disease onset ≤1 month of life (25% vs 1%; P = 0.006). Genetic diagnosis impacted patient management in 11 patients (92%), 7 of whom underwent BMT. CONCLUSION A genetic diagnosis can be established in a significant proportion of suspected monogenic IBD and has an impact on patients' management. Candidate sequencing may be deployed when clinical findings orientate toward a specific diagnosis. Next generation sequencing should be preferred in patients with nonspecific phenotypes.
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Affiliation(s)
- Sara Lega
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Alessia Pin
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Serena Arrigo
- Pediatric Gastroenterology and Endoscopy Unit, Institute Giannina Gaslini, Genoa, Italy
| | - Cristina Cifaldi
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Martina Girardelli
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Anna Monica Bianco
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Monica Malamisura
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Giulia Angelino
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Simona Faraci
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Francesca Rea
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | | | - Marina Aloi
- Pediatric Gastroenterology And Liver Unit, Sapienza University of Rome, Rome, Italy
| | - Claudio Romano
- Pediatric Gastroenterology and Cystic Fibrosis Unit, University of Messina, Messina, Italy
| | - Arrigo Barabino
- Pediatric Gastroenterology and Endoscopy Unit, Institute Giannina Gaslini, Genoa, Italy
| | - Stefano Martelossi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Alberto Tommasini
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | | | - Caterina Cancrini
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Paola De Angelis
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Andrea Finocchi
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Matteo Bramuzzo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
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24
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Zheng Y, Lu Y, Huang X, Han L, Chen Z, Zhou B, Ma Y, Xie G, Yang J, Bian B, Li L, Nie H, Pan X, Shen L. BACH2 regulates the function of human CD4
+
CD45RA
−
Foxp3
l
° cytokine‐secreting T cells and promotes B‐cell response in systemic lupus erythematosus. Eur J Immunol 2020; 50:426-438. [DOI: 10.1002/eji.201948320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/15/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Yingxia Zheng
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
- Institute of Biliary Tract Diseases ResearchShanghai Jiao Tong University School of Medicine Shanghai China
| | - Yiwen Lu
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Xinfang Huang
- Department of NephrologyXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Li Han
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Zheyi Chen
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Bingqian Zhou
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Yanhui Ma
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Guohua Xie
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Junyao Yang
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Bingxian Bian
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Li Li
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Hong Nie
- Shanghai Institute of ImmunologyShanghai Jiao Tong University School of Medicine Shanghai China
| | - Xiujun Pan
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
| | - Lisong Shen
- Department of Laboratory MedicineXin Hua HospitalShanghai Jiao Tong University School of Medicine Shanghai China
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25
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Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao GX, Chan A, Ballesteros Reviriego C, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd CM, Cornall RJ, Maloy KJ, Grencis RK, Griffiths GM, Adams DJ, Hayday AC. High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Nat Immunol 2020; 21:86-100. [PMID: 31844327 PMCID: PMC7338221 DOI: 10.1038/s41590-019-0549-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/29/2019] [Indexed: 01/28/2023]
Abstract
By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic 'hits', of which most had no previous immunologic association. Furthermore, hits were collectively enriched in genes for which humans show poor tolerance to loss of function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with each other and with specific physiologic traits. Such linkages limit freedom of movement for individual immune parameters, thereby imposing genetically regulated 'immunologic structures', the integrity of which was associated with immunocompetence. Hence, we provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.
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Affiliation(s)
| | - Adam G Laing
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Anna Lorenc
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Dmitry S Ushakov
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | | | | | | | | | | | - Namita Saran
- Department of Immunobiology, King's College London, London, UK
| | | | - Belén Morón
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jua Iwasaki
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Philippa R Barton
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Susana Caetano
- Department of Immunobiology, King's College London, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Keng I Hng
- Department of Immunobiology, King's College London, London, UK
| | | | - Simon Forman
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | | | | | | | | | | | - Kolawole O Babalola
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jonathan Warren
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jeremy C Mason
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Amrutha Meeniga
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Natasha A Karp
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | - Brian Weinrick
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Albina Rahim
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Meskas
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Alice Yue
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Markus Lux
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Anna Chan
- Department of Immunobiology, King's College London, London, UK
| | | | | | | | | | - Matthew Edmans
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | | | - Markus Pasztorek
- Department of Immunobiology, King's College London, London, UK
- Department of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Terrence F Meehan
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ryan Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | | | - William Jacobs
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kevin J Maloy
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gillian M Griffiths
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | | | - Adrian C Hayday
- Department of Immunobiology, King's College London, London, UK.
- The Francis Crick Institute, London, UK.
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26
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The Critical Role of Bach2 in Shaping the Balance between CD4 + T Cell Subsets in Immune-Mediated Diseases. Mediators Inflamm 2019; 2019:2609737. [PMID: 32082072 PMCID: PMC7012215 DOI: 10.1155/2019/2609737] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 01/12/2023] Open
Abstract
The transcription factor Bach2 which is predominantly expressed in B and T lymphocytes represses the expression of genes by forming heterodimers with small Maf and Batf proteins and binding to the corresponding sequence on the DNA. In this way, Bach2 serves as a highly conserved repressor which controls the terminal differentiation and maturation of both B and T lymphocytes. It is required for class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes in activated B cells, and its function in B cell differentiation has been well-described. Furthermore, emerging data show that Bach2 regulates transcriptional activity in T cells at super enhancers or regions of high transcriptional activity, thus stabilizing immunoregulatory capacity and maintaining T cell homeostasis. Bach2 is also critical for the formation and function of CD4+ T cell lineages (Th1, Th2, Th9, Th17, T follicular helper (Tfh), and regulatory T (Treg) cells). Genetic variations within Bach2 locus are associated with numerous immune-mediated diseases including multiple sclerosis (MS), rheumatoid arthritis (RA), chronic pancreatitis (CP), type 2 chronic airway inflammation, inflammatory bowel disease (IBD), and type 1 diabetes. Here, we reveal a critical role of Bach2 in regulating T cell biology and the correlation with these immune-mediated diseases.
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27
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[Construction of rat interleukin-10 adenoviral vector and its expression in bone marrow mesenchymal stem cells]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21. [PMID: 31315773 PMCID: PMC7389103 DOI: 10.7499/j.issn.1008-8830.2019.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To construct the recombinant adenoviral vector carrying the rat interleukin-10 (rIL-10) gene, and to investigate whether it is stably expressed in bone marrow mesenchymal stem cells. METHODS The rIL-10 gene was amplified by PCR from template rIL-10 cDNA, and the recovered 656 bp rIL-10 DNA fragment was cloned into pcDNA3.1 to construct pcDNA3.1-IL-10. Then HEK293 cells were transfected with pcDNA3.1-IL-10 and adenoviral vector for homologous recombination, and sequencing and PCR were used to evaluate whether recombination was successful. HEK293 cells were lysed by repeated freeze-thaw cycles, and bone marrow mesenchymal stem cells were infected with the virus solution containing the rIL-10 gene. Western blot was used to measure the expression of rIL-10 in bone marrow mesenchymal stem cells. RESULTS Sequencing and PCR verified that the rIL-10 adenoviral vector was successfully constructed, with a virus titer of 4×109 PFU/mL. The expression of IL-10 was detected after bone marrow mesenchymal stem cells were infected by the virus solution containing the rIL-10 gene. CONCLUSIONS The constructed rIL-10 recombinant adenovirus can mediate the stable expression of rIL-10 gene in bone marrow mesenchymal stem cells, which provides a basis for gene transplantation therapy of inflammatory bowel disease.
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Zheng C, Huang Y, Hu W, Shi J, Ye Z, Qian X, Huang Z, Xue A, Wang Y, Lu J, Tang Z, Wu J, Wang L, Peng K, Zhou Y, Miao S, Sun H. Phenotypic Characterization of Very Early-Onset Inflammatory Bowel Disease with Interleukin-10 Signaling Deficiency: Based on a Large Cohort Study. Inflamm Bowel Dis 2019; 25:756-766. [PMID: 30212871 DOI: 10.1093/ibd/izy289] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Interleukin-10 (IL10)/interleukin-10 receptor (IL10R) deficiency is a rare disease with life-threatening infantile-onset colitis. We sought to accurately phenotype this disorder based on a large cohort of patients with a proven defect of IL10 signaling and to clarify the effects of allogeneic hematopoietic stem cell transplantation (HSCT). METHODS We analyzed the phenotypes of our 61 patients and reviewed 78 other previously reported cases with identified mutations in the genes encoding IL10 or IL10R. We also compared the clinical features of patients with interleukin-10 receptor B (IL10RB), interleukin-10 receptor A (IL10RA), and IL10 mutations. The therapeutic effects of allogeneic HSCT were evaluated. RESULTS We found that the disease onset time was extremely early: 70.3% within 30 days postnatal and 94.9% within the first 6 months of life. In addition, 94.2% of patients typically presented with perianal lesions. Oral ulcers and skin rash were common extra-intestinal manifestations (33.8% and 51.8%, respectively). There was no statistically significant difference in disease onset time, perianal lesion involvement, or mortality rate among patients with IL10RB, IL10RA, or IL10 deficiency. However, the surgery rate was higher in patients with IL10RB mutations than in those with IL10 or IL10RA mutations (P < 0.05). Compared with those with IL10RA deficiency, a higher percentage (32%, 9 of 28) of patients with IL10RB mutations developed B-cell lymphoma (P < 0.01). Compared with other regions, a higher percentage (98.7%) of IL10RA mutations was detected among patients in East Asia countries (P < 0.01), with hot-spot mutation sites of c.C301T and c.G537A. Allogeneic HSCT is efficacious but has a high mortality rate (17.5%, 7 of 40). CONCLUSIONS Our study expands the current knowledge on the genotype-correlated phenotypes with a defect of IL10 signaling. B-cell lymphoma was more frequent than would be expected in patients with IL10RB mutations. There may be a unique genetic architecture among Eastern Asia compared with other populations. Although allogeneic HSCT represents a causal therapeutic approach for IL10-and IL10R-deficient patients, a word of caution is warranted.
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Affiliation(s)
- Cuifang Zheng
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ying Huang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhui Hu
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jieru Shi
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ziqing Ye
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaowen Qian
- Department of Hematology & Oncology, Children's Hospital of Fudan University, Shanghai, China
| | - Zhiheng Huang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Aijuan Xue
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yuhuan Wang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Junping Lu
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Zifei Tang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jie Wu
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Wang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kaiyue Peng
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ying Zhou
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Shijian Miao
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Hua Sun
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
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29
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Lahmann A, Kuhrau J, Fuhrmann F, Heinrich F, Bauer L, Durek P, Mashreghi MF, Hutloff A. Bach2 Controls T Follicular Helper Cells by Direct Repression of Bcl-6. THE JOURNAL OF IMMUNOLOGY 2019; 202:2229-2239. [DOI: 10.4049/jimmunol.1801400] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/27/2019] [Indexed: 12/11/2022]
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30
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de Castro JAL, Stratikos E. Intracellular antigen processing by ERAP2: Molecular mechanism and roles in health and disease. Hum Immunol 2018; 80:310-317. [PMID: 30414458 DOI: 10.1016/j.humimm.2018.11.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/19/2018] [Accepted: 11/05/2018] [Indexed: 02/05/2023]
Abstract
Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) is an intracellular enzyme localized in the ER that has been shown to play roles in the generation of peptides that serve as ligands for MHC class I (MHC-1) molecules. Although ERAP2 has been primarily described as an accessory and complementary enzyme to the homologous ERAP1, several lines of evidence during the last few years suggest that it can play distinct and important roles in processing antigenic peptides and influencing cellular cytotoxic immune responses. Such emerging evidence has been shaping ERAP2 as a potentially tractable target for regulating select autoimmune and anti-cancer responses for therapeutic purposes. Here, we review the state-of-the-art knowledge on the role of ERAP2 in antigen processing, its structure and molecular mechanism, influence on shaping MHC-I-bound immunopeptidomes and its involvement in disease pathogenesis.
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Affiliation(s)
- José A López de Castro
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma), Madrid, Spain.
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, Athens, Greece.
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31
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Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability. G3-GENES GENOMES GENETICS 2018; 8:2881-2888. [PMID: 30166421 PMCID: PMC6118318 DOI: 10.1534/g3.118.200404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Crohn’s disease is a complex genetic trait characterized by chronic relapsing intestinal inflammation. Genome wide association studies (GWAS) have identified more than 170 loci associated with the disease, accounting for ∼14% of the disease variance. We hypothesized that rare genetic variation in GWAS positional candidates also contribute to disease pathogenesis. We performed targeted, massively-parallel sequencing of 101 genes in 205 children with Crohn’s disease, including 179 parent-child trios and 200 controls, both of European ancestry. We used the gene burden test implemented in VAAST and estimated effect sizes using logistic regression and meta-analyses. We identified three genes with nominally significant p-values: NOD2, RTKN2, and MGAT3. Only NOD2 was significant after correcting for multiple comparisons. We identified eight novel rare variants in NOD2 that are likely disease-associated. Incorporation of rare variation and compound heterozygosity nominally increased the proportion of variance explained from 0.074 to 0.089. We estimated the population attributable risk and total heritability of variation in NOD2 to be 32.9% and 3.4%, respectively, with 3.7% and 0.25% accounted for by rare putatively functional variants. Sequencing probands (as opposed to genotyping) to identify rare variants and incorporating phase by sequencing parents can recover a portion of the missing heritability of Crohn’s disease.
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32
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Aridor M. COPII gets in shape: Lessons derived from morphological aspects of early secretion. Traffic 2018; 19:823-839. [DOI: 10.1111/tra.12603] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/26/2018] [Accepted: 07/04/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Meir Aridor
- Department of Cell Biology; University of Pittsburgh School of Medicine; Pittsburgh Pennsylvania
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Mercer CL, Andreoletti G, Carroll A, Salmon AP, Temple IK, Ennis S. Familial Ebstein Anomaly: Whole Exome Sequencing Identifies Novel Phenotype Associated With FLNA. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.116.001683. [PMID: 29237676 DOI: 10.1161/circgenetics.116.001683] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Familial Ebstein anomaly is a rare form of congenital heart disease. We report 7 individuals among 2 generations of 1 family with Ebstein anomaly. This family was first reported in 1991 by Balaji et al in which family members were also reported to have a mild skeletal phenotype. The most likely mechanism of inheritance was concluded to be autosomal dominant. We sought to identify the genetic pathogenesis in this family using a next generation sequencing approach. METHODS AND RESULTS Whole exome sequencing was performed in 2 cousins in this family using the Agilent SureSelect Human all Exon 51 Mb version 5 capture kit. Data were processed through an analytic in-house pipeline. Whole exome sequencing identified a missense mutation in FLNA (Filamin A), an actin-binding protein located at Xq28, mutations in which are associated with the skeletal phenotypes Frontometaphyseal dysplasia, Otopalatodigital, and Melnick-Needles syndrome, with X-linked periventricular nodular heterotopia and FG syndrome (Omim, 305450). Review of the phenotypes of those with the mutation in this family shows increased severity of the cardiac phenotype and associated skeletal features in affected males, consistent with X-linked inheritance. CONCLUSIONS Although congenital heart disease is reported in families with mutations in FLNA, this is the first report of individuals being affected by Ebstein anomaly because of a mutation in this gene and details the concurrent skeletal phenotype observed in this family.
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Affiliation(s)
- Catherine L Mercer
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.).
| | - Gaia Andreoletti
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.).
| | - Aisling Carroll
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - Anthony P Salmon
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - I Karen Temple
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
| | - Sarah Ennis
- From the Wessex Clinical Genetics Service (C.L.M., I.K.T.) and Wessex Cardiac Unit (A.C., A.P.S.), University Hospital Southampton National Health Service Foundation Trust, United Kingdom; and Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, United Kingdom (G.A., I.K.T., S.E.)
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Wang XQ, Xiao Y, Xu X, Yu Y, Shan CY, Guo Y, Gong L, Zhou T, Gao SS, Yuan YZ, Wang XJ, Xu CD. Study of disease phenotype and its association with prognosis of paediatric inflammatory bowel disease in China. BMC Pediatr 2018; 18:229. [PMID: 30001197 PMCID: PMC6044010 DOI: 10.1186/s12887-018-1212-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/06/2018] [Indexed: 02/08/2023] Open
Abstract
Background To investigate the unique features of inflammatory bowel disease (IBD) in children, we wanted to identify whether there might be a strong correlation between the disease phenotype and its prognosis at various ages in paediatric patients. Methods We collected data from patients diagnosed with IBD (ulcerative colitis (UC) or Crohn’s disease (CD)) from 2002 to 2016. The diagnosis was made according to the Porto criteria and Paris Classification. Patient characteristics, clinical manifestations and treatments were collected. Risk factors for surgery, mortality and relapse were analysed by Cox proportional hazard models. Results Of the 143 patients, 113 had CD, and 30 had UC; there were 89 males and 54 females with a median age of 9 years (y). Thirteen patients in the 0–2 y group were identified as having mutations in IL-10 receptor A, and this mutation was significantly more common in this age group than in 3–9 and 10–16 y patients. The risk factor for surgery was the B3 phenotype; risk factors for death were age 0–2 y and B3 phenotype; 0–2 y, B3 phenotype and steroid dependency were risk factors for early relapse. Conclusions Clinical manifestations of the onset of IBD in infants and toddlers were extensive and aggressive and were closely associated with early relapse and death. It is of particular interest that some of these patients developed IBD due to monogenic disorders; thus, introduction of genetic testing is essential for these patients.
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Affiliation(s)
- Xin-Qiong Wang
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Yuan Xiao
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Xu Xu
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Yi Yu
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Cheng-Yan Shan
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Yan Guo
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Ling Gong
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Tong Zhou
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Shen-Shen Gao
- Department of Paediatrics, Ruijin Hospital North, Shanghai Jiao Tong University, School of Medicine, Shanghai, 201821, China
| | - Yao-Zong Yuan
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Xiao-Jin Wang
- Department of Biostatistics, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Chun-Di Xu
- Department of Paediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, No. 197, Rui Jin Er Road, Shanghai, 200025, China. .,Department of Paediatrics, Ruijin Hospital North, Shanghai Jiao Tong University, School of Medicine, Shanghai, 201821, China.
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Liefferinckx C, Franchimont D. Viewpoint: Toward the Genetic Architecture of Disease Severity in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2018; 24:1428-1439. [PMID: 29788122 DOI: 10.1093/ibd/izy109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is characterized by uneven disease courses with various clinical outcomes. A few prognostic markers of disease severity may help stratify patients and identify those who will benefit the most from early aggressive treatment. The concept of disease severity remains too broad and vague, mainly because the definition must embrace several disease mechanisms, mainly inflammation and fibrosis, with various rates of disease progression. The magnitude of inflammation is an obvious key driver of disease severity in IBD that ultimately influence disease behavior. Advances in the genetics underlying disease severity are currently emerging, but attempts to overlap the genetics of disease susceptibility and severity have until now been unsatisfactory, suggesting that the genetic architecture of disease severity may be distinct from the genetics of disease susceptibility. In this review, we report on the current knowledge on disease severity and on the main research venues to decipher the genetic architecture of disease severity.
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Affiliation(s)
| | - Denis Franchimont
- Department of Gastroenterology, Erasme Hospital, ULB, Brussels, Belgium
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36
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Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt MT, Krawczak M, Schreiber S, Rosenstiel P. Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease. Gut 2017; 66:2087-2097. [PMID: 27694142 PMCID: PMC5749366 DOI: 10.1136/gutjnl-2016-311651] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/15/2016] [Accepted: 08/14/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVE An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD. DESIGN Mucosal biopsies from Crohn's disease and patients with UC, disease controls and healthy individuals (n=63) were subjected to microbiome, transcriptome and splicing analysis, employing next-generation sequencing. The three data levels were integrated by different bioinformatic approaches, including systems biology-inspired network and pathway analysis. RESULTS Microbiota, host transcript levels and host splicing patterns were influenced most strongly by tissue differences, followed by the effect of inflammation. Both factors point towards a substantial disease-related alteration of metabolic processes. We also observed a strong enrichment of splicing events in inflamed tissues, accompanied by an alteration of the mucosa-attached bacterial taxa. Finally, we noted a striking uncoupling of the three molecular entities when moving from healthy individuals via disease controls to patients with IBD. CONCLUSIONS Our results provide strong evidence that the interplay between microbiome and host transcriptome, which normally characterises a state of intestinal homeostasis, is drastically perturbed in Crohn's disease and UC. Consequently, integrating multiple OMICs levels appears to be a promising approach to further disentangle the complexity of IBD.
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Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Carolin Knecht
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Berenice Brandt
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Sascha Schäuble
- Language and Information Engineering Lab, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Fretter
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany,Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
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37
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Petersen BS, August D, Abt R, Alddafari M, Atarod L, Baris S, Bhavsar H, Brinkert F, Buchta M, Bulashevska A, Chee R, Cordeiro AI, Dara N, Dückers G, Elmarsafy A, Frede N, Galal N, Gerner P, Glocker EO, Goldacker S, Hammermann J, Hasselblatt P, Havlicekova Z, Hübscher K, Jesenak M, Karaca NE, Karakoc-Aydiner E, Kharaghani MM, Kilic SS, Kiykim A, Klein C, Klemann C, Kobbe R, Kotlarz D, Laass MW, Leahy TR, Mesdaghi M, Mitton S, Neves JF, Öztürk B, Pereira LF, Rohr J, Restrepo JLR, Ruzaike G, Saleh N, Seneviratne S, Senol E, Speckmann C, Tegtmeyer D, Thankam P, van der Werff Ten Bosch J, von Bernuth H, Zeissig S, Zeissig Y, Franke A, Grimbacher B. Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea. Inflamm Bowel Dis 2017; 23:2109-2120. [PMID: 28930861 DOI: 10.1097/mib.0000000000001235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients. METHODS We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients. RESULTS Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients. CONCLUSIONS Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.
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Affiliation(s)
- Britt-Sabina Petersen
- 1Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany; 2Center for Chronic Immunodeficiency (CCI), DZIF Satellite Center, Medical Center, Faculty of Medicine, Germany; 3Paediatric Gastroenterology, Klinikum Nürnberg, Nuremberg, Germany; 4Laboratory of Applied Molecular Biology and Immunology, University of Abou-Bekr Belkaïd, Tlemcen, Algeria; 5Department of Pediatrics, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; 6Clinic of Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey; 7Department of Gastroenterology and Clinical Nutrition, Birmingham Children's Hospital, Birmingham, United Kingdom; 8Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; 9Department of Immunology, Royal Free Hospital, London, United Kingdom; 10Primary Immunodeficiencies Unit, Hospital Dona Estefania, Pediatric University Hospital, and CEDOC, Chronic Diseases Research Center, NOVA Medical School, Lisbon, Portugal; 11Department of Pediatric Gasteroentrology and Hepatology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 12Helios Kliniken, Childrens Hospital, Krefeld, Germany; 13Pediatrics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; 14Paediatric Gastroenterology/Hepatology, University of Freiburg, Freiburg, Germany; 15Institute of Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany; 16Department of Pediatrics, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 17Department of Medicine II, University Hospital and Medical Faculty, University Freiburg, Freiburg, Germany; 18Department of Paediatrics, Centre for Diagnosis and Treatment of Primary Immunodeficiencies, Jessenius Faculty of Medicine, Commenius University in Bratislava, Martin, Slovakia; 19Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey; 20Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 21Pediatric Immunology Division, Uludag University Medical Faculty, Department of Pediatrics, Bursa, Turkey; 22Dr. von Hauner Children's Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität Munich, Munich, Germany; 23Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 24Center for Pediatrics, Department of Pediatric Hematology and Oncology, University Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 25Department of Paediatric Immunology and Infectious Diseases, Our Lady's Children's Hospital, Dublin, Ireland; 26Department of Immunology, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 27Department of Paediatric Gastroenterology, St. George's Healthcare NHS Trust and University of London, London, United Kingdom; 28Department of Gastroenterology and Clinical Nutrition, Marmara University Medical Faculty, Istanbul, Turkey; 29Service of Clinical Laboratory, Division of Immunology, San Pedro De Alcántara Hospital, Cáceres, Spain; 30Bone Marrow Failure Group, Division of Pediatric Hematology and Oncology, University of Freiburg, Germany; 31Children's Hospital, University of Bonn, Germany; 32University College London Institute of Immunity and Transplantation, Royal Free Campus, London, United Kingdom; 33Department of Paediatrics, St. George's Hospital, University of London, London, United Kingdom; 34Department of Pediatrics, Universitair Ziekenhuis Brussel, Brussels, Belgium; 35Pediatric Pneumology and Immunology, Department of Immunology, Charité University Medicine Labor Berlin Charité Vivantes GmbH, Berlin, Germany; 36Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 37Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany; and 38Institute of Laboratory Medicine, Brandenburg Hospital, Brandenburg Medical School, Brandenburg/Havel, Germany
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Abstract
Inflammatory bowel disease (IBD), including Crohn disease and ulcerative colitis, is characterized by chronic intestinal inflammation due to a complex interaction of genetic determinants, disruption of mucosal barriers, aberrant inflammatory signals, loss of tolerance, and environmental triggers. Importantly, the incidence of pediatric IBD is rising, particularly in children younger than 10 years. In this review, we discuss the clinical presentation of these patients and highlight environmental exposures that may affect disease risk, particularly among people with a background genetic risk. With regard to both children and adults, we review advancements in understanding the intestinal epithelium, the mucosal immune system, and the resident microbiota, describing how dysfunction at any level can lead to diseases like IBD. We conclude with future directions for applying advances in IBD genetics to better understand pathogenesis and develop therapeutics targeting key pathogenic nodes.
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Affiliation(s)
- Joanna M Peloquin
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Gautam Goel
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Eduardo J Villablanca
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , ,
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease and.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.,Harvard Medical School, Boston, Massachusetts 02115; , , , .,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02142.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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39
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Ashton JJ, Ennis S, Beattie RM. Early-onset paediatric inflammatory bowel disease. THE LANCET CHILD & ADOLESCENT HEALTH 2017; 1:147-158. [DOI: 10.1016/s2352-4642(17)30017-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 06/08/2017] [Accepted: 06/14/2017] [Indexed: 12/27/2022]
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40
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Raghavan N, Tosto G. Genetics of Alzheimer's Disease: the Importance of Polygenic and Epistatic Components. Curr Neurol Neurosci Rep 2017; 17:78. [PMID: 28825204 PMCID: PMC5699909 DOI: 10.1007/s11910-017-0787-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW We aimed to summarize the recent advances in genetic findings of Alzheimer's disease (AD), focusing on traditional single-marker and gene approaches and non-traditional ones, i.e., polygenic and epistatic components. RECENT FINDINGS Genetic studies have progressed over the last few decades from linkage to genome-wide association studies (GWAS), and most recently studies utilizing high-throughput sequencing. So far, GWASs have identified several common variants characterized by small effect sizes (besides APOE-ε4). Sequencing has facilitated the study of rare variants with larger effects. Nevertheless, missing heritability for AD remains extensive; a possible explanation might lie in the existence of polygenic and epistatic components. We review findings achieved by single-marker approaches, but also polygenic and epistatic associations. The latter two are critical, yet-underexplored mechanisms. Genes involved in complex diseases are likely regulated by mechanisms and pathways involving many other genes, an aspect potentially missed by traditional approaches.
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Affiliation(s)
- Neha Raghavan
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, NY, 10032, USA
- Institute for Genomic Medicine, Columbia University, New York, NY, 10032, USA
| | - Giuseppe Tosto
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA.
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York, NY, 10032, USA.
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 622 W. 168th Street PH 19-314, New York, NY, 10032, USA.
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41
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Uhlig HH, Muise AM. Clinical Genomics in Inflammatory Bowel Disease. Trends Genet 2017; 33:629-641. [PMID: 28755896 DOI: 10.1016/j.tig.2017.06.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/25/2017] [Accepted: 06/27/2017] [Indexed: 12/19/2022]
Abstract
Genomic technologies inform the complex genetic basis of polygenic inflammatory bowel disease (IBD) as well as Mendelian disease-associated IBD. Aiming to diagnose patients that present with extreme phenotypes due to monogenic forms of IBD, genomics has progressed from 'orphan disease' research towards an integrated standard of clinical care. Advances in diagnostic clinical genomics are increasingly complemented by pathway-specific therapies that aim to correct the consequences of genetic defects. This highlights the exceptional potential for personalized precision medicine. IBD is nevertheless a challenging example for genomic medicine because the overall fraction of patients with Mendelian defects is low, the number of potential candidate genes is high, and interventional evidence is still emerging. We discuss requirements and prospects of explanatory and predictive clinical genomics in IBD.
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Affiliation(s)
- Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, UK; Department of Paediatrics, University of Oxford, UK.
| | - Aleixo M Muise
- Program in Cell Biology, Research Institute, Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada; SickKids Inflammatory Bowel Disease Centre and Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
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42
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Lin Z, Wang Z, Hegarty JP, Lin TR, Wang Y, Deiling S, Wu R, Thomas NJ, Floros J. Genetic association and epistatic interaction of the interleukin-10 signaling pathway in pediatric inflammatory bowel disease. World J Gastroenterol 2017; 23:4897-4909. [PMID: 28785144 PMCID: PMC5526760 DOI: 10.3748/wjg.v23.i27.4897] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/18/2017] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To study the genetic association and epistatic interaction of the interleukin (IL)-10 and IL-10/STAT3 pathways in pediatric inflammatory bowel disease (IBD).
METHODS A total of 159 pediatric inflammatory IBD patients (Crohn’s disease, n = 136; ulcerative colitis, n = 23) and 129 matched controls were studied for genetic association of selected single nucleotide polymorphisms (SNPs) of the IL-10 gene and the genes IL10RA, IL10RB, STAT3, and HO1, from the IL-10/STAT3 signaling pathway. As interactions between SNPs from different loci may significantly affect the associated risk for disease, additive (a) and dominant (d) modeling of SNP interactions was also performed to examine high-order epistasis between combinations of the individual SNPs.
RESULTS The results showed that IL-10 rs304496 was associated with pediatric IBD (P = 0.022), but no association was found for two other IL-10 SNPs, rs1800872 and rs2034498, or for SNPs in genes IL10RA, IL10RB, STAT3, and HO1. However, analysis of epistatic interaction among these genes showed significant interactions: (1) between two IL-10 SNPs rs1800872 and rs3024496 (additive-additive P = 0.00015, Bonferroni P value (Bp) = 0.003); (2) between IL-10RB rs2834167 and HO1 rs2071746 (dominant-additive, P = 0.0018, Bp = 0.039); and (3) among IL-10 rs1800872, IL10RB rs2834167, and HO1 rs2071746 (additive-dominant-additive, P = 0.00015, Bp = 0.005), as well as weak interactions among IL-10 rs1800872, IL-10 rs3024496, and IL-10RA (additive-additive-additive, P = 0.003; Bp = 0.099), and among IL10RA, IL10RB, and HO1 genes (additive-dominant-additive, P = 0.008, Bp = 0.287).
CONCLUSION These results indicate that both the IL-10 gene itself, and through epistatic interaction with genes within the IL-10/STAT3 signaling pathway, contribute to the risk of pediatric IBD.
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Igarashi K, Kurosaki T, Roychoudhuri R. BACH transcription factors in innate and adaptive immunity. Nat Rev Immunol 2017; 17:437-450. [PMID: 28461702 DOI: 10.1038/nri.2017.26] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BTB and CNC homology (BACH) proteins are transcriptional repressors of the basic region leucine zipper (bZIP) transcription factor family. Recent studies indicate widespread roles of BACH proteins in controlling the development and function of the innate and adaptive immune systems, including the differentiation of effector and memory cells of the B and T cell lineages, CD4+ regulatory T cells and macrophages. Here, we emphasize similarities at a molecular level in the cell-type-specific activities of BACH factors, proposing that competitive interactions of BACH proteins with transcriptional activators of the bZIP family form a common mechanistic theme underlying their diverse actions. The findings contribute to a general understanding of how transcriptional repressors shape lineage commitment and cell-type-specific functions through repression of alternative lineage programmes.
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Affiliation(s)
- Kazuhiko Igarashi
- Department of Biochemistry, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tomohiro Kurosaki
- Laboratory for Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi-ku, Yokohama 230-0045, Japan
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
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44
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Sasikala M, Ravikanth VV, Murali Manohar K, Deshpande N, Singh S, Pavan Kumar P, Talukdar R, Ghosh S, Aslam M, Rao GV, Pradeep R, Reddy DN. Bach2 repression mediates Th17 cell induced inflammation and associates with clinical features of advanced disease in chronic pancreatitis. United European Gastroenterol J 2017; 6:272-282. [PMID: 29511557 DOI: 10.1177/2050640617716596] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/25/2017] [Indexed: 12/29/2022] Open
Abstract
Objectives Altered immune homeostasis and involvement of T cells has been reported in chronic pancreatitis (CP). We evaluated the role of Bach2 (BTB and CNC homology basic leucine zipper transcription factor 2), a key regulator of immune homeostasis in the chronicity of CP. Methods Expression of Bach2 and T-cell transcription factors, enumeration of BACH2+/CD4+ T-lymphocytes were performed by qRT-PCR and flow cytometry respectively. Bach2silenced human CD4+ T-lymphocytes were exposed to CP tissue extract to assess T-cell lineage commitment. Aryl hydrocarbon receptor (Ahr) and Deubiquitinase enzyme A (DUBA/OTUD5gene) were evaluated as markers of persistent Th17 cell differentiation. Bach2 gene (exons) was sequenced to identify risk variants and functionally validated. Results Decrease in Bach2 (p < 0.0001) and increase (p < 0.001) in TBX21, RORC, Ahr, PRDM1, IL23R mRNA were noted in pancreatic tissues, while BACH2+/CD4+ T-lymphocytes were decreased (p < 0.01) in circulation and tissues. Exposure of Bach2 silenced CD4+ T-lymphocytes to CP tissue extract showed increased Ahr, decreased OTUD5, and enhanced Th17 cell differentiation. Sequencing of Bach2 gene revealed association of novel variant (rs9111 in 5'-UTR) with advanced disease and luciferase assay confirmed its role in Bach2 repression. Conclusion Bach2 repression mediates Th17 cell induced inflammation and rs9111-TT in individuals with primary genetic susceptibility to CP is associated with clinical features of advanced disease.
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Affiliation(s)
- M Sasikala
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - V V Ravikanth
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - K Murali Manohar
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - Neha Deshpande
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - Sandhya Singh
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - P Pavan Kumar
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - R Talukdar
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - Sudip Ghosh
- National Institute of Nutrition, Tarnaka, Hyderabad, India Equally contributed to the study and shared first authorship
| | - Mohsin Aslam
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - G V Rao
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - R Pradeep
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
| | - D Nageshwar Reddy
- Asian Healthcare Foundation, Asian Institute of Gastroenterology, Somajiguda, India
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Exome Analysis of Rare and Common Variants within the NOD Signaling Pathway. Sci Rep 2017; 7:46454. [PMID: 28422189 PMCID: PMC5396125 DOI: 10.1038/srep46454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/20/2017] [Indexed: 02/06/2023] Open
Abstract
Pediatric inflammatory bowel disease (pIBD) is a chronic heterogeneous disorder. This study looks at the burden of common and rare coding mutations within 41 genes comprising the NOD signaling pathway in pIBD patients. 136 pIBD and 106 control samples underwent whole-exome sequencing. We compared the burden of common, rare and private mutation between these two groups using the SKAT-O test. An independent replication cohort of 33 cases and 111 controls was used to validate significant findings. We observed variation in 40 of 41 genes comprising the NOD signaling pathway. Four genes were significantly associated with disease in the discovery cohort (BIRC2 p = 0.004, NFKB1 p = 0.005, NOD2 p = 0.029 and SUGT1 p = 0.047). Statistical significance was replicated for BIRC2 (p = 0.041) and NOD2 (p = 0.045) in an independent validation cohort. A gene based test on the combined discovery and replication cohort confirmed association for BIRC2 (p = 0.030). We successfully applied burden of mutation testing that jointly assesses common and rare variants, identifying two previously implicated genes (NFKB1 and NOD2) and confirmed a possible role in disease risk in a previously unreported gene (BIRC2). The identification of this novel gene provides a wider role for the inhibitor of apoptosis gene family in IBD pathogenesis.
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Douglas AGL, Andreoletti G, Talbot K, Hammans SR, Singh J, Whitney A, Ennis S, Foulds NC. ADCY5-related dyskinesia presenting as familial myoclonus-dystonia. Neurogenetics 2017; 18:111-117. [PMID: 28229249 PMCID: PMC5359383 DOI: 10.1007/s10048-017-0510-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 11/29/2022]
Abstract
We describe a family with an autosomal dominant familial dyskinesia resembling myoclonus-dystonia associated with a novel missense mutation in ADCY5, found through whole-exome sequencing. A tiered analytical approach was used to analyse whole-exome sequencing data from an affected grandmother-granddaughter pair. Whole-exome sequencing identified 18,000 shared variants, of which 46 were non-synonymous changes not present in a local cohort of control exomes (n = 422). Further filtering based on predicted splicing effect, minor allele frequency in the 1000 Genomes Project and on phylogenetic conservation yielded 13 candidate variants, of which the heterozygous missense mutation c.3086T>G, p. M1029R in ADCY5 most closely matched the observed phenotype. This report illustrates the utility of whole-exome sequencing in cases of undiagnosed movement disorders with clear autosomal dominant inheritance. Moreover, ADCY5 mutations should be considered in cases with apparent myoclonus-dystonia, particularly where SCGE mutations have been excluded. ADCY5-related dyskinesia may manifest variable expressivity within a single family, and affected individuals may be initially diagnosed with differing neurological phenotypes.
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Affiliation(s)
- Andrew G L Douglas
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Level G, Mailpoint 627, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA, UK
| | - Gaia Andreoletti
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Simon R Hammans
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jaspal Singh
- Paediatric Neurology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andrea Whitney
- Paediatric Neurology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sarah Ennis
- Academic Unit of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Level G, Mailpoint 627, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA, UK.
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Takahashi S, Andreoletti G, Chen R, Munehira Y, Batra A, Afzal NA, Beattie RM, Bernstein JA, Ennis S, Snyder M. De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease. Genome Med 2017; 9:8. [PMID: 28126021 PMCID: PMC5270254 DOI: 10.1186/s13073-016-0394-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/23/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well understood. METHODS We performed a family-based whole exome sequencing (WES) analysis on a core family (Family A) to identify potential causal mutations and then analyzed exome data from a Caucasian pediatric cohort (136 patients and 106 controls) to validate the presence of mutations in the candidate gene, heat shock 70 kDa protein 1-like (HSPA1L). Biochemical assays of the de novo and rare (minor allele frequency, MAF < 0.01) mutation variant proteins further validated the predicted deleterious effects of the identified alleles. RESULTS In the proband of Family A, we found a heterozygous de novo mutation (c.830C > T; p.Ser277Leu) in HSPA1L. Through analysis of WES data of 136 patients, we identified five additional rare HSPA1L mutations (p.Gly77Ser, p.Leu172del, p.Thr267Ile, p.Ala268Thr, p.Glu558Asp) in six patients. In contrast, rare HSPA1L mutations were not observed in controls, and were significantly enriched in patients (P = 0.02). Interestingly, we did not find non-synonymous rare mutations in the HSP70 isoforms HSPA1A and HSPA1B. Biochemical assays revealed that all six rare HSPA1L variant proteins showed decreased chaperone activity in vitro. Moreover, three variants demonstrated dominant negative effects on HSPA1L and HSPA1A protein activity. CONCLUSIONS Our results indicate that de novo and rare mutations in HSPA1L are associated with IBD and provide insights into the pathogenesis of IBD, and also expand our understanding of the roles of HSP70s in human disease.
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Affiliation(s)
- Shinichi Takahashi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Rare Disease & LCM Laboratories, R & D Division, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Gaia Andreoletti
- Human Genetics and Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Rui Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoichi Munehira
- Department of Biology, Stanford University, Stanford, CA, USA.,Oncology Laboratories, Oncology Function, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Akshay Batra
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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48
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Seaby EG, Gilbert RD, Andreoletti G, Pengelly RJ, Mercer C, Hunt D, Ennis S. Unexpected Findings in a Child with Atypical Hemolytic Uremic Syndrome: An Example of How Genomics Is Changing the Clinical Diagnostic Paradigm. Front Pediatr 2017; 5:113. [PMID: 28589114 PMCID: PMC5438966 DOI: 10.3389/fped.2017.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/01/2017] [Indexed: 12/17/2022] Open
Abstract
CBL is a tumor suppressor gene on chromosome 11 encoding a multivalent adaptor protein with E3 ubiquitin ligase activity. Germline CBL mutations are dominant. Pathogenic de novo mutations result in a phenotype that overlaps Noonan syndrome (1). Some patients with CBL mutations go on to develop juvenile myelomonocytic leukemia (JMML), an aggressive malignancy that usually necessitates bone marrow transplantation. Using whole exome sequencing methods, we identified a known mutation in CBL in a 4-year-old Caucasian boy with atypical hemolytic uremic syndrome, moyamoya phenomenon, and dysmorphology consistent with a mild Noonan-like phenotype. Exome data revealed loss of heterozygosity across chromosome 11q consistent with JMML but in the absence of clinical leukemia. Our finding challenges conventional clinical diagnostics since we have identified a pathogenic variant in the CBL gene previously only ascertained in children presenting with leukemia. The increasing affordability of expansive sequencing is likely to increase the scope of clinical profiles observed for previously identified pathogenic variants and calls into question the interpretability and indications for clinical management.
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Affiliation(s)
- Eleanor G Seaby
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rodney D Gilbert
- Wessex Regional Paediatric Nephro-Urology Service, Southampton Children's Hospital, Southampton, UK.,Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gaia Andreoletti
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Reuben J Pengelly
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catherine Mercer
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
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49
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Norouzinia M, Chaleshi V, Alizadeh AHM, Zali MR. Biomarkers in inflammatory bowel diseases: insight into diagnosis, prognosis and treatment. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2017; 10:155-167. [PMID: 29118930 PMCID: PMC5660264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic disease of unknown etiology which mostly involves the intestine and requires a personalized approach for treatment. IBD represents a heterogeneous group of patients with inherently variable disease courses. Hence, the heterogeneity of patient populations may delay the diagnosis, clinical practice and initiation of appropriate treatment. Use of biomarkers for diagnosis and management of IBD is still necessary. Descriptions of the immunological pathway abnormalities in IBD improve assessment to identify the patient's disease status, and relative risk of progression to complicated disease behaviors, and this information may ultimately influence therapeutic decisions. In this study, we try to explain the role of biomarkers in early diagnosis, estimating prognosis, and target agents for correct managements of IBD's patients. This information might be important to provide insight into emerging panels of multiple IBD biomarkers and highlighting the essential role of personalizes panel for each patient.
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Affiliation(s)
- Mohsen Norouzinia
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Chaleshi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Houshang Mohammad Alizadeh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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50
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Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population. Sci Rep 2016; 6:39831. [PMID: 28008999 PMCID: PMC5180213 DOI: 10.1038/srep39831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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