1
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Qiao Y, Tang X, Liu Z, Ocansey DKW, Zhou M, Shang A, Mao F. Therapeutic Prospects of Mesenchymal Stem Cell and Their Derived Exosomes in the Regulation of the Gut Microbiota in Inflammatory Bowel Disease. Pharmaceuticals (Basel) 2024; 17:607. [PMID: 38794176 PMCID: PMC11124012 DOI: 10.3390/ph17050607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Mesenchymal stem cells (MSCs) have shown great potential in the treatment of several inflammatory diseases due to their immunomodulatory ability, which is mediated by exosomes secreted by MSCs (MSC-Exs). The incidence of inflammatory bowel disease (IBD) is increasing globally, but there is currently no long-term effective treatment. As an emerging therapy, MSC-Exs have proven to be effective in alleviating IBD experimentally, and the specific mechanism continues to be explored. The gut microbiota plays an important role in the occurrence and development of IBD, and MSCs and MSC-Exs can effectively regulate gut microbiota in animal models of IBD, but the mechanism involved and whether the outcome can relieve the characteristic dysbiosis necessary to alleviate IBD still needs to be studied. This review provides current evidence on the effective modulation of the gut microbiota by MSC-Exs, offering a basis for further research on the pathogenic mechanism of IBD and MSC-Ex treatments through the improvement of gut microbiota.
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Affiliation(s)
- Yaru Qiao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
| | - Xiaohua Tang
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang 212300, China;
| | - Ziyue Liu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
| | - Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Medical Laboratory Science, School of Allied Health Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast CC0959347, Ghana
| | - Mengjiao Zhou
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
| | - Anquan Shang
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Y.Q.); (Z.L.); (D.K.W.O.); (M.Z.)
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang 222006, China;
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2
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Jia K, Shen J. Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives. Cell Biosci 2024; 14:29. [PMID: 38403629 PMCID: PMC10895848 DOI: 10.1186/s13578-024-01204-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Crohn's disease (CD) is regarded as a lifelong progressive disease affecting all segments of the intestinal tract and multiple organs. Based on genome-wide association studies (GWAS) and gene expression data, transcriptome-wide association studies (TWAS) can help identify susceptibility genes associated with pathogenesis and disease behavior. In this review, we overview seven reported TWASs of CD, summarize their study designs, and discuss the key methods and steps used in TWAS, which affect the prioritization of susceptibility genes. This article summarized the screening of tissue-specific susceptibility genes for CD, and discussed the reported potential pathological mechanisms of overlapping susceptibility genes related to CD in a certain tissue type. We observed that ileal lipid-related metabolism and colonic extracellular vesicles may be involved in the pathogenesis of CD by performing GO pathway enrichment analysis for susceptibility genes. We further pointed the low reproducibility of TWAS associated with CD and discussed the reasons for these issues, strategies for solving them. In the future, more TWAS are needed to be designed into large-scale, unified cohorts, unified analysis pipelines, and fully classified databases of expression trait loci.
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Affiliation(s)
- Keyu Jia
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China
| | - Jun Shen
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Research Center, Ren Ji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China.
- NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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3
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Kumar S, Ahmad MF, Nath P, Roy R, Bhattacharjee R, Shama E, Gahatraj I, Sehrawat M, Dasriya V, Dhillon HS, Puniya M, Samtiya M, Dhewa T, Aluko RE, Khedkar GD, Raposo A, Puniya AK. Controlling Intestinal Infections and Digestive Disorders Using Probiotics. J Med Food 2023; 26:705-720. [PMID: 37646629 DOI: 10.1089/jmf.2023.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
After consumption, probiotics provide health benefits to the host. Probiotics and their metabolites have therapeutic and nutritional properties that help to alleviate gastrointestinal, neurological, and cardiovascular problems. Probiotics strengthen host immunity through various mechanisms, including improved gut barrier function, receptor site blocking, competitive exclusion of pathogens, and the production of bioactive molecules. Emerging evidence suggests that intestinal bowel diseases can be fatal, but regular probiotic consumption can alleviate disease symptoms. The use and detailed description of the health benefits of probiotics to consumers in terms of reducing intestinal infection, inflammation, and digestive disorders are discussed in this review. The well-designed and controlled studies that examined the use of probiotics to reduce life-threatening activities caused by intestinal bowel diseases are also covered. This review discussed the active principles and potency of probiotics as evidenced by the known effects on host health, in addition to providing information on the mechanism of action.
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Affiliation(s)
- Sanjeev Kumar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Md Faruque Ahmad
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Priyakshi Nath
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Rubina Roy
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Rudrarup Bhattacharjee
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Eman Shama
- Department of Clinical Nutrition, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Indira Gahatraj
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | | | - Vaishali Dasriya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | | | - Monica Puniya
- Science and Standards Division, Food Safety and Standards Authority of India, New Delhi, India
| | - Mrinal Samtiya
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
| | - Tejpal Dhewa
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Canada
| | - Gulab D Khedkar
- Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
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4
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Otte ML, Lama Tamang R, Papapanagiotou J, Ahmad R, Dhawan P, Singh AB. Mucosal healing and inflammatory bowel disease: Therapeutic implications and new targets. World J Gastroenterol 2023; 29:1157-1172. [PMID: 36926666 PMCID: PMC10011951 DOI: 10.3748/wjg.v29.i7.1157] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/16/2022] [Accepted: 02/14/2023] [Indexed: 02/21/2023] Open
Abstract
Mucosal healing (MH) is vital in maintaining homeostasis within the gut and protecting against injury and infections. Multiple factors and signaling pathways contribute in a dynamic and coordinated manner to maintain intestinal homeostasis and mucosal regeneration/repair. However, when intestinal homeostasis becomes chronically disturbed and an inflammatory immune response is constitutively active due to impairment of the intestinal epithelial barrier autoimmune disease results, particularly inflammatory bowel disease (IBD). Many proteins and signaling pathways become dysregulated or impaired during these pathological conditions, with the mechanisms of regulation just beginning to be understood. Consequently, there remains a relative lack of broadly effective therapeutics that can restore MH due to the complexity of both the disease and healing processes, so tissue damage in the gastrointestinal tract of patients, even those in clinical remission, persists. With increased understanding of the molecular mechanisms of IBD and MH, tissue damage from autoimmune disease may in the future be ameliorated by developing therapeutics that enhance the body’s own healing response. In this review, we introduce the concept of mucosal healing and its relevance in IBD as well as discuss the mechanisms of IBD and potential strategies for altering these processes and inducing MH.
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Affiliation(s)
- Megan Lynn Otte
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Raju Lama Tamang
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Julia Papapanagiotou
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Amar B Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
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5
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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6
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Lu G, Wang Y, Shi Y, Zhang Z, Huang C, He W, Wang C, Shen HM. Autophagy in health and disease: From molecular mechanisms to therapeutic target. MedComm (Beijing) 2022; 3:e150. [PMID: 35845350 PMCID: PMC9271889 DOI: 10.1002/mco2.150] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 02/05/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionally conserved catabolic process in which cytosolic contents, such as aggregated proteins, dysfunctional organelle, or invading pathogens, are sequestered by the double‐membrane structure termed autophagosome and delivered to lysosome for degradation. Over the past two decades, autophagy has been extensively studied, from the molecular mechanisms, biological functions, implications in various human diseases, to development of autophagy‐related therapeutics. This review will focus on the latest development of autophagy research, covering molecular mechanisms in control of autophagosome biogenesis and autophagosome–lysosome fusion, and the upstream regulatory pathways including the AMPK and MTORC1 pathways. We will also provide a systematic discussion on the implication of autophagy in various human diseases, including cancer, neurodegenerative disorders (Alzheimer disease, Parkinson disease, Huntington's disease, and Amyotrophic lateral sclerosis), metabolic diseases (obesity and diabetes), viral infection especially SARS‐Cov‐2 and COVID‐19, cardiovascular diseases (cardiac ischemia/reperfusion and cardiomyopathy), and aging. Finally, we will also summarize the development of pharmacological agents that have therapeutic potential for clinical applications via targeting the autophagy pathway. It is believed that decades of hard work on autophagy research is eventually to bring real and tangible benefits for improvement of human health and control of human diseases.
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Affiliation(s)
- Guang Lu
- Department of Physiology, Zhongshan School of Medicine Sun Yat-sen University Guangzhou China
| | - Yu Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Yin Shi
- Department of Biochemistry Zhejiang University School of Medicine Hangzhou China
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Weifeng He
- State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Burn Research Southwest Hospital Army Medical University Chongqing China
| | - Chuang Wang
- Department of Pharmacology, Provincial Key Laboratory of Pathophysiology Ningbo University School of Medicine Ningbo Zhejiang China
| | - Han-Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology University of Macau Macau China
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7
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He W, Gao Y, Zhou J, Shi Y, Xia D, Shen HM. Friend or Foe? Implication of the autophagy-lysosome pathway in SARS-CoV-2 infection and COVID-19. Int J Biol Sci 2022; 18:4690-4703. [PMID: 35874956 PMCID: PMC9305279 DOI: 10.7150/ijbs.72544] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/24/2022] [Indexed: 12/14/2022] Open
Abstract
There is increasing amount of evidence indicating the close interplays between the replication cycle of SARS-CoV-2 and the autophagy-lysosome pathway in the host cells. While autophagy machinery is known to either assist or inhibit the viral replication process, the reciprocal effects of the SARS-CoV-2 on the autophagy-lysosome pathway have also been increasingly appreciated. More importantly, despite the disappointing results from the clinical trials of chloroquine and hydroxychloroquine in treatment of COVID-19, there is still ongoing effort in discovering new therapeutics targeting the autophagy-lysosome pathway. In this review, we provide an update-to-date summary of the interplays between the autophagy-lysosome pathway in the host cells and the pathogen SARS-CoV-2 at the molecular level, to highlight the prognostic value of autophagy markers in COVID-19 patients and to discuss the potential of developing novel therapeutic strategies for COVID-19 by targeting the autophagy-lysosome pathway. Thus, understanding the nature of such interactions between SARS-CoV-2 and the autophagy-lysosome pathway in the host cells is expected to provide novel strategies in battling against this global pandemic.
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Affiliation(s)
- Weifeng He
- State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Burn Research, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yuan Gao
- Faculty of Health Sciences, University of Macau, Macau, China.,Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jing Zhou
- Department of Physiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi Province, China
| | - Yi Shi
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Dajing Xia
- Department of Toxicology of School of Public Health, Department of Gynecologic Oncology of Women's Hospital; Department of Central Laboratory, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
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8
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Okai N, Watanabe T, Minaga K, Kamata K, Honjo H, Kudo M. Alterations of autophagic and innate immune responses by the Crohn’s disease-associated ATG16L1 mutation. World J Gastroenterol 2022; 28:3063-3070. [PMID: 36051337 PMCID: PMC9331526 DOI: 10.3748/wjg.v28.i26.3063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/21/2022] [Accepted: 06/16/2022] [Indexed: 02/06/2023] Open
Abstract
Crohn’s disease (CD) is driven by the loss of tolerance to intestinal microbiota and excessive production of pro-inflammatory cytokines. These pro-inflammatory cytokines are produced by macrophages and dendritic cells (DCs) upon sensing the intestinal microbiota by the pattern recognition receptors (PRRs). Impaired activation of PRR-mediated signaling pathways is associated with chronic gastrointestinal inflammation, as shown by the fact that loss-of-function mutations in the nucleotide-binding oligomerization domain 2 gene increase the risk of CD development. Autophagy is an intracellular degradation process, during which cytoplasmic nutrients and intracellular pathogens are digested. Given that impaired reaction to intestinal microbiota alters signaling pathways mediated by PRRs, it is likely that dysfunction of the autophagic machinery is involved in the development of CD. Indeed, the loss-of-function mutation T300A in the autophagy related 16 like 1 (ATG16L1) protein, a critical regulator of autophagy, increases susceptibility to CD. Recent studies have provided evidence that ATG16L1 is involved not only in autophagy, but also in PRR-mediated signaling pathways. ATG16L1 negatively regulates pro-inflammatory cytokine responses of macrophages and DCs after these cells sense the intestinal microbiota by PRRs. Here, we discuss the molecular mechanisms underlying the development of CD in the T300A ATG16L1 mutation by focusing on PRR-mediated signaling pathways.
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Affiliation(s)
- Natsuki Okai
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
| | - Tomohiro Watanabe
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
| | - Kosuke Minaga
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
| | - Ken Kamata
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
| | - Hajime Honjo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama 589-8511, Osaka, Japan
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9
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Lapaquette P, Bizeau JB, Acar N, Bringer MA. Reciprocal interactions between gut microbiota and autophagy. World J Gastroenterol 2021; 27:8283-8301. [PMID: 35068870 PMCID: PMC8717019 DOI: 10.3748/wjg.v27.i48.8283] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/09/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
A symbiotic relationship has set up between the gut microbiota and its host in the course of evolution, forming an interkingdom consortium. The gut offers a favorable ecological niche for microbial communities, with the whole body and external factors (e.g., diet or medications) contributing to modulating this microenvironment. Reciprocally, the gut microbiota is important for maintaining health by acting not only on the gut mucosa but also on other organs. However, failure in one or another of these two partners can lead to the breakdown in their symbiotic equilibrium and contribute to disease onset and/or progression. Several microbial and host processes are devoted to facing up the stress that could alter the symbiosis, ensuring the resilience of the ecosystem. Among these processes, autophagy is a host catabolic process integrating a wide range of stress in order to maintain cell survival and homeostasis. This cytoprotective mechanism, which is ubiquitous and operates at basal level in all tissues, can be rapidly down- or up-regulated at the transcriptional, post-transcriptional, or post-translational levels, to respond to various stress conditions. Because of its sensitivity to all, metabolic-, immune-, and microbial-derived stimuli, autophagy is at the crossroad of the dialogue between changes occurring in the gut microbiota and the host responses. In this review, we first delineate the modulation of host autophagy by the gut microbiota locally in the gut and in peripheral organs. Then, we describe the autophagy-related mechanisms affecting the gut microbiota. We conclude this review with the current challenges and an outlook toward the future interventions aiming at modulating host autophagy by targeting the gut microbiota.
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Affiliation(s)
- Pierre Lapaquette
- UMR PAM A 02.102, University Bourgogne Franche-Comté, Agrosup Dijon, Dijon 21000, France
| | - Jean-Baptiste Bizeau
- Eye and Nutrition Research Group, Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Niyazi Acar
- Eye and Nutrition Research Group, Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Marie-Agnès Bringer
- Eye and Nutrition Research Group, Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, Dijon 21000, France
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10
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Zou M, Zeng QS, Nie J, Yang JH, Luo ZY, Gan HT. The Role of E3 Ubiquitin Ligases and Deubiquitinases in Inflammatory Bowel Disease: Friend or Foe? Front Immunol 2021; 12:769167. [PMID: 34956195 PMCID: PMC8692584 DOI: 10.3389/fimmu.2021.769167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/17/2021] [Indexed: 02/05/2023] Open
Abstract
Inflammatory bowel disease (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), exhibits a complex multifactorial pathogenesis involving genetic susceptibility, imbalance of gut microbiota, mucosal immune disorder and environmental factors. Recent studies reported associations between ubiquitination and deubiquitination and the occurrence and development of inflammatory bowel disease. Ubiquitination modification, one of the most important types of post-translational modifications, is a multi-step enzymatic process involved in the regulation of various physiological processes of cells, including cell cycle progression, cell differentiation, apoptosis, and innate and adaptive immune responses. Alterations in ubiquitination and deubiquitination can lead to various diseases, including IBD. Here, we review the role of E3 ubiquitin ligases and deubiquitinases (DUBs) and their mediated ubiquitination and deubiquitination modifications in the pathogenesis of IBD. We highlight the importance of this type of posttranslational modification in the development of inflammation, and provide guidance for the future development of targeted therapeutics in IBD.
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Affiliation(s)
- Min Zou
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Qi-Shan Zeng
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Nie
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Jia-Hui Yang
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen-Yi Luo
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Hua-Tian Gan
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
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11
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Caparrós E, Wiest R, Scharl M, Rogler G, Gutiérrez Casbas A, Yilmaz B, Wawrzyniak M, Francés R. Dysbiotic microbiota interactions in Crohn's disease. Gut Microbes 2021; 13:1949096. [PMID: 34313550 PMCID: PMC8320851 DOI: 10.1080/19490976.2021.1949096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Crohn's disease (CD) is a major form of inflammatory bowel disease characterized by transmural inflammation along the alimentary tract. Changes in the microbial composition and reduction in species diversity are recognized as pivotal hallmarks in disease dynamics, challenging the gut barrier function and shaping a pathological immune response in genetically influenced subjects. The purpose of this review is to delve into the modification of the gut microbiota cluster network during CD progression and to discuss how this shift compromises the gut barrier integrity, granting the translocation of microbes and their products. We then complete the scope of the review by retracing gut microbiota dysbiosis interactions with the main pathophysiologic factors of CD, starting from the host's genetic background to the immune inflammatory and fibrotic processes, providing a standpoint on the lifestyle/exogenous factors and the potential benefits of targeting a specific gut microbiota.
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Affiliation(s)
- Esther Caparrós
- Dpto Medicina Clínica, Universidad Miguel Hernández, San Juan De Alicante, Spain,Iis Isabial, Hospital General Universitario De Alicante, Alicante, Spain
| | - Reiner Wiest
- Department for Biomedical Research, Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Ana Gutiérrez Casbas
- Iis Isabial, Hospital General Universitario De Alicante, Alicante, Spain,CIBERehd, Instituto De Salud Carlos III, Madrid, Spain
| | - Bahtiyar Yilmaz
- Department for Biomedical Research, Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marcin Wawrzyniak
- Department of Gastroenterology and Hepatology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Rubén Francés
- Dpto Medicina Clínica, Universidad Miguel Hernández, San Juan De Alicante, Spain,Iis Isabial, Hospital General Universitario De Alicante, Alicante, Spain,CIBERehd, Instituto De Salud Carlos III, Madrid, Spain,CONTACT Rubén Francés Hepatic and Intestinal Immunobiology Group. Departamento De Medicina Clínica, Universidad Miguel Hernández De Elche. Carretera Alicante-Valencia, Km 8,703550San Juan De Alicante
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12
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Snyder EF, Davis S, Aldrich K, Veerabagu M, Larussa T, Abenavoli L, Boccuto L. Crohn disease: Identification, diagnosis, and clinical management. Nurse Pract 2021; 46:22-30. [PMID: 34808643 DOI: 10.1097/01.npr.0000798212.61425.4f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACT Crohn disease is an inflammatory bowel disorder affecting children and adults. With its increasing prevalence, healthcare providers need adequate resources to assist with diagnosis and management. This article discusses early diagnosis, disease severity and classification, familial predisposition and genomics, and clinical management in the primary care setting.
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13
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Kocot AM, Wróblewska B. Fermented products and bioactive food compounds as a tool to activate autophagy and promote the maintenance of the intestinal barrier function. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Otten AT, Bourgonje AR, Peters V, Alizadeh BZ, Dijkstra G, Harmsen HJM. Vitamin C Supplementation in Healthy Individuals Leads to Shifts of Bacterial Populations in the Gut-A Pilot Study. Antioxidants (Basel) 2021; 10:antiox10081278. [PMID: 34439526 PMCID: PMC8389205 DOI: 10.3390/antiox10081278] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Gut microbes are crucial to human health, but microbial composition is often disturbed in a number of human diseases. Accumulating evidence points to nutritional modulation of the gut microbiota as a potentially beneficial therapeutic strategy. Vitamin C (ascorbic acid) may be of particular interest as it has known antioxidant and anti-inflammatory properties. In this study, we investigated whether supplementation with high-dose vitamin C may favourably affect the composition of the gut microbiota. In this pilot study, healthy human participants received 1000 mg vitamin C supplementation daily for two weeks. Gut microbiota composition was analysed before and after intervention by performing faecal 16S rRNA gene sequencing. In total, 14 healthy participants were included. Daily supplementation of high-dose vitamin C led to an increase in the relative abundances of Lachnospiraceae (p < 0.05), whereas decreases were observed for Bacteroidetes (p < 0.01), Enterococci (p < 0.01) and Gemmiger formicilis (p < 0.05). In addition, trends for bacterial shifts were observed for Blautia (increase) and Streptococcus thermophilus (decrease). High-dose vitamin C supplementation for two weeks shows microbiota-modulating effects in healthy individuals, with several beneficial shifts of bacterial populations. This may be relevant as these bacteria have anti-inflammatory properties and strongly associate with gut health.
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Affiliation(s)
- Antonius T. Otten
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Arno R. Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Vera Peters
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands; (A.T.O.); (A.R.B.); (V.P.); (G.D.)
| | - Hermie J. M. Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Correspondence: ; Tel.: +31-50-361-3480
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15
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Danne C, Rolhion N, Sokol H. Recipient factors in faecal microbiota transplantation: one stool does not fit all. Nat Rev Gastroenterol Hepatol 2021; 18:503-513. [PMID: 33907321 DOI: 10.1038/s41575-021-00441-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
Faecal microbiota transplantation (FMT) is a promising therapy for chronic diseases associated with gut microbiota alterations. FMT cures 90% of recurrent Clostridioides difficile infections. However, in complex diseases, such as inflammatory bowel disease, irritable bowel syndrome and metabolic syndrome, its efficacy remains variable. It is accepted that donor selection and sample administration are key determinants of FMT success, yet little is known about the recipient factors that affect it. In this Perspective, we discuss the effects of recipient parameters, such as genetics, immunity, microbiota and lifestyle, on donor microbiota engraftment and clinical efficacy. Emerging evidence supports the possibility that controlling inflammation in the recipient intestine might facilitate engraftment by reducing host immune system pressure on the newly transferred microbiota. Deciphering FMT engraftment rules and developing novel therapeutic strategies are priorities to alleviate the burden of chronic diseases associated with an altered gut microbiota such as inflammatory bowel disease.
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Affiliation(s)
- Camille Danne
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France.,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France
| | - Nathalie Rolhion
- Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France.,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France
| | - Harry Sokol
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France. .,Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France. .,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, Paris, France. .,French Group of Fecal Microbiota Transplantation (GFTF), Paris, France. .,AP-HP Fecal Microbiota transplantation Center, Saint Antoine Hospital, Paris, France.
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16
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Prins MMC, Giugliano FP, van Roest M, van de Graaf SFJ, Koelink PJ, Wildenberg ME. Thiopurines correct the effects of autophagy impairment on intestinal healing - a potential role for ARHGAP18/RhoA. Dis Model Mech 2021; 14:258489. [PMID: 33973626 PMCID: PMC8084572 DOI: 10.1242/dmm.047233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
The ATG16L1 T300A single-nucleotide polymorphism (SNP) is associated with Crohn's disease and causes an autophagy impairment. We have previously shown that this SNP is involved in the migration and hyperactivation of Rac1 in dendritic cells. Mucosal healing, currently the main target for inflammatory bowel disease treatment, depends on restoration of the epithelial barrier and requires appropriate migration of epithelial cells towards and over mucosal lesions. Therefore, we here further investigated the impact of autophagy on epithelial migration. ATG16L1 knockdown was established in the HT29 human colonic epithelial cell line using lentiviral transduction. Migratory capacity was evaluated using scratch assays and RhoAGTP was measured using G-LISA. Immunofluorescent ARHGAP18 and sequestome 1 (SQSTM1; also known as p62) staining was performed on HT29 cells and primary colonic tissue of Crohn's disease patients. We observed that ATG16L1 knockdown cells exhibited decreased autophagy and decreased migration capacity. Furthermore, activity of RhoA was decreased. These characteristics were phenocopied using ATG5 knockdown and pharmacological inhibition of autophagy. The migration defect was dependent on accumulation of SQSTM1 and was alleviated upon SQSTM1 knockdown. Strikingly, thiopurines also mitigated the effects of impaired autophagy. RhoA dysregulation appeared mediated through accumulation of the upstream regulator ARHGAP18, which was observed in cell lines, human foetal organoids and primary colonic tissue. Our results indicate that the ATG16L1 T300A Crohn's disease-associated SNP causes a decrease in migration capacity in epithelial cells, mediated by an increase in SQSTM1 and ARHGAP18 protein and subsequent reduced RhoA activation.
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Affiliation(s)
- Marileen M C Prins
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Francesca P Giugliano
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Manon van Roest
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Pim J Koelink
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers (UMC), location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam UMC, location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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17
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Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK. Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut 2021; 70:285-296. [PMID: 32651235 PMCID: PMC7815889 DOI: 10.1136/gutjnl-2019-319706] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD. DESIGN To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics. RESULTS We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15. CONCLUSION This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Christine Stevens
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Laura Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hendrik van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutic, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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18
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Rayner JO, Roberts RA, Kim J, Poklepovic A, Roberts JL, Booth L, Dent P. AR12 (OSU-03012) suppresses GRP78 expression and inhibits SARS-CoV-2 replication. Biochem Pharmacol 2020; 182:114227. [PMID: 32966814 PMCID: PMC7502229 DOI: 10.1016/j.bcp.2020.114227] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
Abstract
AR12 is a derivative of celecoxib which no-longer acts against COX2 but instead inhibits the ATPase activity of multiple chaperone proteins, in particular GRP78. GRP78 acts as a sensor of endoplasmic reticulum stress and is an essential chaperone required for the life cycle of all mammalian viruses. We and others previously demonstrated in vitro and in vivo that AR12 increases autophagosome formation and autophagic flux, enhances virus protein degradation, preventing virus reproduction, and prolonging the survival of infected animals. In this report, we determined whether AR12 could act against SARS-CoV-2. In a dose-dependent fashion AR12 inhibited SARS-CoV-2 spike protein expression in transfected or infected cells. AR12 suppressed the production of infectious virions via autophagosome formation, which was also associated with degradation of GRP78. After AR12 exposure, the colocalization of GRP78 with spike protein was reduced. Knock down of eIF2α prevented AR12-induced spike degradation and knock down of Beclin1 or ATG5 caused the spike protein to localize in LAMP2+ vesicles without apparent degradation. HCT116 cells expressing ATG16L1 T300, found in the majority of persons of non-European descent, particularly from Africa, expressed greater amounts of GRP78 and SARS-CoV-2 receptor angiotensin converting enzyme 2 compared to ATG16L1 A300, predominantly found in Europeans, suggestive that ATG16L1 T300 expression may be associated with a greater ability to be infected and to reproduce SARS-CoV-2. In conclusion, our findings demonstrate that AR12 represents a clinically relevant anti-viral drug for the treatment of SARS-CoV-2.
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Affiliation(s)
- Jonathan O Rayner
- Department of Microbiology and Immunology, Laboratory of Infectious Diseases, University of South Alabama, Mobile, AL 36688-0002, United States
| | - Rosemary A Roberts
- Department of Microbiology and Immunology, Laboratory of Infectious Diseases, University of South Alabama, Mobile, AL 36688-0002, United States
| | - Jin Kim
- Department of Microbiology and Immunology, Laboratory of Infectious Diseases, University of South Alabama, Mobile, AL 36688-0002, United States
| | - Andrew Poklepovic
- Departments of Medicine, Virginia Commonwealth University, Richmond, VA 23298-0035, United States
| | - Jane L Roberts
- Departments of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298-0035, United States
| | - Laurence Booth
- Departments of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298-0035, United States
| | - Paul Dent
- Departments of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298-0035, United States.
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19
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Pai YC, Weng LT, Wei SC, Wu LL, Shih DQ, Targan SR, Turner JR, Yu LCH. Gut microbial transcytosis induced by tumor necrosis factor-like 1A-dependent activation of a myosin light chain kinase splice variant contributes to IBD. J Crohns Colitis 2020; 15:jjaa165. [PMID: 32770194 PMCID: PMC7904084 DOI: 10.1093/ecco-jcc/jjaa165] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD) is characterized by abnormal host-microbe interactions. Proinflammatory cytokine IFNγ and a novel TNF superfamily member, TL1A, have been implicated in epithelial barrier dysfunction. The divergent regulatory mechanisms of transcellular versus paracellular hyperpermeability remain poorly understood. Intestinal epithelia express two splice variants of long myosin light chain kinase (MLCK), of which the full-length MLCK1 differ from the shorter isoform MLCK2 by a Src kinase phosphorylation site. The aim was to investigate the roles of MLCK splice variants in gut barrier defects under proinflammatory stress. Upregulated expression of TL1A, IFNγ, and two MLCK variants was observed in human IBD biopsy specimens. The presence of intraepithelial bacteria preceded tight junction (TJ) damage in dextran sodium sulfate-treated and TL1A-transgenic mouse models. Lack of barrier defects was observed in long MLCK(-/-) mice. TL1A induced MLCK-dependent terminal web (TW) contraction, brush border fanning, and transepithelial bacterial internalization. The bacterial taxa identified in the inflamed colonocytes included Escherichia, Enterococcus, Staphylococcus,and Lactobacillus. Recombinant TL1A and IFNγ at low doses induced PI3K/Akt/MLCK2-dependent bacterial endocytosis, whereas high-dose IFNγ caused TJ opening via the iNOS/Src/MLCK1 axis. Bacterial internalization was recapitulated in MLCK-knockout cells individually expressing MLCK2 but not MLCK1. Immunostaining showed different subcellular sites of phosphorylated MLC localized to the TJ and TW in the MLCK1- and MLCK2-expressing cells, respectively. In conclusion, proinflammatory cytokines induced bacterial influx through transcellular and paracellular routes via divergent pathways orchestrated by distinct MLCK isoforms. Bacterial transcytosis induced by TL1A may be an alternative route causing symptom flares in IBD.
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Affiliation(s)
- Yu-Chen Pai
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Ting Weng
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Chen Wei
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Ling Wu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Physiology, Yang-Ming University, Taipei, Taiwan
| | - David Q Shih
- Inflammatory Bowel and Immunobiology Research Institute, Cedar-Sinai Medical Center, Los Angeles, California, USA
| | - Stephen R Targan
- Inflammatory Bowel and Immunobiology Research Institute, Cedar-Sinai Medical Center, Los Angeles, California, USA
| | - Jerrold R Turner
- Brigham’s Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan
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20
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Nasef NA, Mehta S. Role of Inflammation in Pathophysiology of Colonic Disease: An Update. Int J Mol Sci 2020; 21:E4748. [PMID: 32635383 PMCID: PMC7370289 DOI: 10.3390/ijms21134748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Diseases of the colon are a big health burden in both men and women worldwide ranging from acute infection to cancer. Environmental and genetic factors influence disease onset and outcome in multiple colonic pathologies. The importance of inflammation in the onset, progression and outcome of multiple colonic pathologies is gaining more traction as the evidence from recent research is considered. In this review, we provide an update on the literature to understand how genetics, diet, and the gut microbiota influence the crosstalk between immune and non‑immune cells resulting in inflammation observed in multiple colonic pathologies. Specifically, we focus on four colonic diseases two of which have a more established association with inflammation (inflammatory bowel disease and colorectal cancer) while the other two have a less understood relationship with inflammation (diverticular disease and irritable bowel syndrome).
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Affiliation(s)
- Noha Ahmed Nasef
- Riddet Institute, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Sunali Mehta
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Biodiscovery, University of Otago, Dunedin 9054, New Zealand
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21
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Xue AJ, Miao SJ, Sun H, Qiu XX, Wang SN, Wang L, Ye ZQ, Zheng CF, Huang ZH, Wang YH, Huang Y. Intestinal dysbiosis in pediatric Crohn's disease patients with IL10RA mutations. World J Gastroenterol 2020; 26:3098-3109. [PMID: 32587451 PMCID: PMC7304104 DOI: 10.3748/wjg.v26.i22.3098] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/30/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Several studies have employed animal models to explore the association between microbiota and interleukin (IL) 10 signaling; however, limited information is available about the human microbiome.
AIM To characterize the microbiome in patients with IL10RA mutations and to explore the association between gut dysbiosis and disease severity.
METHODS Fecal samples were collected from patients who were diagnosed with loss-of-function mutations in the IL10RA gene between January 2017 and July 2018 at the Children's Hospital of Fudan University. Age-matched volunteer children were recruited as healthy controls. Patients with Crohn's disease (CD) were used as disease controls to standardize the antibiotic exposure. Microbial DNA was extracted from the fecal samples. All analyses were based on the 16S rRNA gene sequencing data.
RESULTS Seventeen patients with IL10RA mutations (IL10RA group), 17 patients with pediatric CD, and 26 healthy children were included. Both patients with IL10RA mutations and those with CD exhibited a reduced diversity of gut microbiome with increased variability. The relative abundance of Firmicutes was substantially increased in the IL10RA group (P = 0.02). On further comparison of the relative abundance of taxa between patients with IL10RA mutations and healthy children, 13 taxa showed significant differences. The IL10RA-specific dysbiosis indices exhibited a significant positive correlation with weighted pediatric CD activity index and simple endoscopic score for CD.
CONCLUSION In patients with IL10RA mutations and early onset inflammatory bowel disease, gut dysbiosis shows a moderate association with disease severity.
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Affiliation(s)
- Ai-Juan Xue
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Shi-Jian Miao
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Hua Sun
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Xiao-Xia Qiu
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Sheng-Nan Wang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Lin Wang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Zi-Qing Ye
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Cui-Fang Zheng
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Zhi-Heng Huang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Yu-Huan Wang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
| | - Ying Huang
- Department of Gastroenterology, Children’s Hospital of Fudan University, Shanghai 201102, China
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Sun R, Abraham C. IL23 Promotes Antimicrobial Pathways in Human Macrophages, Which Are Reduced With the IBD-Protective IL23R R381Q Variant. Cell Mol Gastroenterol Hepatol 2020; 10:673-697. [PMID: 32474165 PMCID: PMC7490566 DOI: 10.1016/j.jcmgh.2020.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Interleukin (IL)23 is a major contributor to inflammatory bowel disease (IBD) pathogenesis and is being pursued as a therapeutic target, both through targeting IL23 alone or in combination with IL12. Unexpected trial outcomes highlight the importance of understanding the cell types through which IL23 regulates immune responses, and how IL23 and IL12 compare in these responses. Macrophages are key players in IBD, and IL23 recently was found to promote inflammatory outcomes in human macrophages. This raises the possibility that IL23 may be required for additional essential macrophage functions, in particular microbial clearance, such that either blocking the IL23 pathway or the IL23R-R381Q IBD-protective variant may reduce macrophage-mediated microbial clearance. METHODS We analyzed protein expression, signaling, bacterial uptake, and intracellular bacterial clearance in human monocyte-derived macrophages through Western blot, flow cytometry, and gentamicin protection. RESULTS Autocrine/paracrine IL23 was critical for optimal levels of pattern-recognition-receptor (PRR)-induced intracellular bacterial clearance in human macrophages. Mechanisms regulated by IL23 included induction of pyruvate dehydrogenase kinase 1-dependent bacterial uptake, and up-regulation of reactive oxygen species through nicotinamide adenine dinucleotide phosphate oxidase members, nitric oxide synthase 2, and autophagy through ATG5 and ATG16L1. Complementing these pathways in IL23R-deficient macrophages restored PRR-induced bacterial uptake and clearance. Janus kinase 2, TYK2, and STAT3 were required for IL23-induced mechanisms. IL23 and IL12 induced antimicrobial pathways to similar levels in human macrophages. Relative to IL23R-R381, transfected IL23R-Q381, or monocyte-derived macrophages from IL23R-Q381 carriers showed reduced bacterial uptake and clearance. CONCLUSIONS We identify that autocrine/paracrine IL23 is required for optimal PRR-enhanced macrophage bacterial uptake and intracellular bacterial clearance, define mechanisms regulating IL23R-induced bacterial clearance, and determine how the IBD-protective IL23R-R381Q variant modulates these processes.
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Affiliation(s)
- Rui Sun
- Section of Digestive Diseases, Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Clara Abraham
- Section of Digestive Diseases, Department of Internal Medicine, Yale University, New Haven, Connecticut.
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Larabi A, Barnich N, Nguyen HTT. New insights into the interplay between autophagy, gut microbiota and inflammatory responses in IBD. Autophagy 2020; 16:38-51. [PMID: 31286804 PMCID: PMC6984609 DOI: 10.1080/15548627.2019.1635384] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023] Open
Abstract
One of the most significant challenges of inflammatory bowel disease (IBD) research is to understand how alterations in the symbiotic relationship between the genetic composition of the host and the intestinal microbiota, under impact of specific environmental factors, lead to chronic intestinal inflammation. Genome-wide association studies, followed by functional studies, have identified a role for numerous autophagy genes in IBD, especially in Crohn disease. Studies using in vitro and in vivo models, in addition to human clinical studies have revealed that autophagy is pivotal for intestinal homeostasis maintenance, gut ecology regulation, appropriate intestinal immune responses and anti-microbial protection. This review describes the latest researches on the mechanisms by which dysfunctional autophagy leads to disrupted intestinal epithelial function, gut dysbiosis, defect in anti-microbial peptide secretion by Paneth cells, endoplasmic reticulum stress response and aberrant immune responses to pathogenic bacteria. A better understanding of the role of autophagy in IBD pathogenesis may provide better sub-classification of IBD phenotypes and novel approaches for disease management.Abbreviations: AIEC: adherent-invasive Escherichia coli; AMPK: AMP-activated protein kinase; ATF6: activating transcription factor 6; ATG: autophagy related; Atg16l1[ΔIEC] mice: mice with Atg16l1 depletion specifically in intestinal epithelial cells; Atg16l1[HM] mice: mice hypomorphic for Atg16l1 expression; BCL2: B cell leukemia/lymphoma 2; BECN1: beclin 1, autophagy related; CALCOCO2: calcium binding and coiled-coil domain 2; CASP: caspase; CD: Crohn disease; CGAS: cyclic GMP-AMP synthase; CHUK/IKKA: conserved helix-loop-helix ubiquitous kinase; CLDN2: claudin 2; DAPK1: death associated protein kinase 1; DCs: dendritic cells; DSS: dextran sulfate sodium; EIF2A: eukaryotic translation initiation factor 2A; EIF2AK: eukaryotic translation initiation factor 2 alpha kinase; ER: endoplasmic reticulum; ERBIN: Erbb2 interacting protein; ERN1/IRE1A: ER to nucleus signaling 1; FNBP1L: formin binding protein 1-like; FOXP3: forkhead box P3; GPR65: G-protein coupled receptor 65; GSK3B: glycogen synthase kinase 3 beta; IBD: inflammatory bowel disease; IECs: intestinal epithelial cells; IFN: interferon; IL: interleukin; IL10R: interleukin 10 receptor; IRGM: immunity related GTPase M; ISC: intestinal stem cell; LAMP1: lysosomal-associated membrane protein 1; LAP: LC3-associated phagocytosis; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; LRRK2: leucine-rich repeat kinase 2; MAPK: mitogen-activated protein kinase; MHC: major histocompatibility complex; MIF: macrophage migration inhibitory factor; MIR/miRNA: microRNA; MTMR3: myotubularin related protein 3; MTOR: mechanistic target of rapamycin kinase; MYD88: myeloid differentiation primary response gene 88; NLRP3: NLR family, pyrin domain containing 3; NOD2: nucleotide-binding oligomerization domain containing 2; NPC: Niemann-Pick disease type C; NPC1: NPC intracellular cholesterol transporter 1; OMVs: outer membrane vesicles; OPTN: optineurin; PI3K: phosphoinositide 3-kinase; PRR: pattern-recognition receptor; PTPN2: protein tyrosine phosphatase, non-receptor type 2; PTPN22: protein tyrosine phosphatase, non-receptor type 22 (lymphoid); PYCARD/ASC: PYD and CARD domain containing; RAB2A: RAB2A, member RAS oncogene family; RELA: v-rel reticuloendotheliosis viral oncogene homolog A (avian); RIPK2: receptor (TNFRSF)-interacting serine-threonine kinase 2; ROS: reactive oxygen species; SNPs: single nucleotide polymorphisms; SQSTM1: sequestosome 1; TAX1BP1: Tax1 binding protein 1; Th: T helper 1; TIRAP/TRIF: toll-interleukin 1 receptor (TIR) domain-containing adaptor protein; TLR: toll-like receptor; TMEM173/STING: transmembrane protein 173; TMEM59: transmembrane protein 59; TNF/TNFA: tumor necrosis factor; Treg: regulatory T; TREM1: triggering receptor expressed on myeloid cells 1; UC: ulcerative colitis; ULK1: unc-51 like autophagy activating kinase 1; WT: wild-type; XBP1: X-box binding protein 1; XIAP: X-linked inhibitor of apoptosis.
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Affiliation(s)
- Anaïs Larabi
- M2iSH, UMR 1071 Inserm, INRA USC 2018, CRNH, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Nicolas Barnich
- M2iSH, UMR 1071 Inserm, INRA USC 2018, CRNH, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Hang Thi Thu Nguyen
- M2iSH, UMR 1071 Inserm, INRA USC 2018, CRNH, University of Clermont Auvergne, Clermont-Ferrand, France
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Should We Divide Crohn's Disease Into Ileum-Dominant and Isolated Colonic Diseases? Clin Gastroenterol Hepatol 2019; 17:2634-2643. [PMID: 31009791 PMCID: PMC6885453 DOI: 10.1016/j.cgh.2019.04.040] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 03/25/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
Crohn's disease (CD) is an inflammatory bowel disease that can involve any region of the gastrointestinal tract. First described in 1932 as terminal ileitis or regional enteritis, it predominately involves the ileum with or without colonic involvement. Isolated colonic CD was first described in 1960 and since then the phenotypic classification of CD has evolved to stratify patients into isolated ileal, ileocolonic, or isolated colonic involvement. In the current review we evaluate the published literature regarding differences in epidemiology, natural history, pathogenesis, response to therapy, and disease monitoring, when stratified by disease location. Based on the available evidence consideration could be given to a new classification for CD, which splits it into ileum dominant (isolated ileal and ileocolonic) and isolated colonic disease. This may allow for a more optimized approach to clinical care and scientific research for CD.
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Aden K, Reindl W. The Gut Microbiome in Inflammatory Bowel Diseases: Diagnostic and Therapeutic Implications. Visc Med 2019; 35:332-337. [PMID: 31934579 PMCID: PMC6944918 DOI: 10.1159/000504148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022] Open
Abstract
The incidence of chronic inflammatory bowel diseases (IBD) is rising worldwide, and the interaction between the mucosal immune system and the intestinal microbiota is crucial for the understanding of these diseases. Due to new technologies, the data published on the intestinal microbiota has increased rapidly in the recent years. While many findings are descriptive, reporting associations between disease and microbial populations, recent advancement in technology made it possible to ask and answer more functional questions and to elucidate complex interactions between the intestinal microbiota and the mucosal immune system. In addition, first trials influenced the intestinal microbiota with the intention to treat IBD. This review summarizes aspects of the physiological function as well as the inflammation-induced changes of the gut microbiota and the association between the gut microbiota and pathogenesis in IBD. In addition, diagnostic and therapeutic options for treating IBD are reviewed.
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Affiliation(s)
- Konrad Aden
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Reindl
- II. Medizinische Klinik, Universitätsmedizin Mannheim, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Germany
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Macrophages Inability to Mediate Adherent-Invasive E. coli Replication is Linked to Autophagy in Crohn's Disease Patients. Cells 2019; 8:cells8111394. [PMID: 31694333 PMCID: PMC6912674 DOI: 10.3390/cells8111394] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/28/2022] Open
Abstract
The macrophages from Crohn’s Disease (CD) patients are defective to control the replication of CD-associated adherent-invasive E. coli (AIEC). We aimed to identify the host factors associated with AIEC replication focusing on polymorphisms related to autophagy. Peripheral blood monocyte-derived macrophages (MDM), obtained from 95 CD patient, 30 ulcerative colitis (UC) patients and 15 healthy subjects, were genotyped for several CD-associated polymorphisms. AIEC bacteria survival increased within MDM from CD patients compared to UC (p = 0.0019). AIEC bacteria survival increased in patients with CD-associated polymorphism IRGM (p = 0.05) and reduced in those with CD-associated polymorphisms XBP-1 (p = 0.026) and ULK-1 (p = 0.033). AIEC infection led to an increase of pro-inflammatory cytokines IL-1β (p < 0.0001) and TNF-α (p < 0.0001) in CD macrophages. ULK-1 expression increased in AIEC-infected MDM from CD patients compared to MDM from UC patients or healthy subjects (p = 0.0056) and correlated with AIEC survival (p = 0.0013). Moreover, the expression of ULK-1 phosphorylation on Serine 757 decreased following to AIEC infection (p < 0.0001). Short-term silencing of ULK-1 and IRGM genes restricted and promote, respectively, AIEC survival within MDM (p = 0.0018 and p = 0.0291). In conclusion, the macrophage defect to mediate AIEC clearance in CD patients is linked to polymorphisms related to autophagy such as IRGM and ULK-1.
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Alsaadi RM, Losier TT, Tian W, Jackson A, Guo Z, Rubinsztein DC, Russell RC. ULK1-mediated phosphorylation of ATG16L1 promotes xenophagy, but destabilizes the ATG16L1 Crohn's mutant. EMBO Rep 2019; 20:e46885. [PMID: 31267703 PMCID: PMC6607016 DOI: 10.15252/embr.201846885] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 04/09/2019] [Accepted: 04/25/2019] [Indexed: 12/19/2022] Open
Abstract
Autophagy is a highly regulated catabolic pathway that is potently induced by stressors including starvation and infection. An essential component of the autophagy pathway is an ATG16L1-containing E3-like enzyme, which is responsible for lipidating LC3B and driving autophagosome formation. ATG16L1 polymorphisms have been linked to the development of Crohn's disease (CD), and phosphorylation of CD-associated ATG16L1 T300A (caATG16L1) has been hypothesized to contribute to cleavage and autophagy dysfunction. Here we show that ULK1 kinase directly phosphorylates ATG16L1 in response to infection and starvation. Phosphorylated ATG16L1 localizes to the site of internalized bacteria and stable cell lines harbouring a phospho-dead mutant of ATG16L1 have impaired xenophagy, indicating a role for ATG16L1 phosphorylation in the promotion of anti-bacterial autophagy. In contrast to wild-type ATG16L1, ULK1-mediated phosphorylation of caATG16L1 drives its destabilization in response to stress. In summary, our results show that ATG16L1 is a novel target of ULK1 kinase and that ULK1 signalling to ATG16L1 is a double-edged sword, enhancing the function of the wild-type ATG16L1, but promoting degradation of caATG16L1.
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Affiliation(s)
- Reham M Alsaadi
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
| | - Truc T Losier
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
| | - Wensheng Tian
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
| | - Anne Jackson
- Department of Medical GeneticsCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Zhihao Guo
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
| | - David C Rubinsztein
- Department of Medical GeneticsCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
- UK Dementia Research InstituteCambridgeUK
| | - Ryan C Russell
- Department of Cellular and Molecular MedicineUniversity of OttawaOttawaONCanada
- Center for Infection, Immunity and InflammationUniversity of OttawaOttawaONCanada
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Neratinib inhibits Hippo/YAP signaling, reduces mutant K-RAS expression, and kills pancreatic and blood cancer cells. Oncogene 2019; 38:5890-5904. [PMID: 31253872 DOI: 10.1038/s41388-019-0849-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022]
Abstract
Prior studies demonstrated that the irreversible ERBB1/2/4 inhibitor neratinib caused plasma membrane-associated mutant K-RAS to localize in intracellular vesicles, concomitant with its degradation. Herein, we discovered that neratinib interacted with the chemically distinct irreversible ERBB1/2/4 inhibitor afatinib to reduce expression of ERBB1, ERBB2, K-RAS and N-RAS; this was associated with greater-than-additive cell killing of pancreatic tumor cells. Knock down of Beclin1, ATG16L1, Rubicon or cathepsin B significantly lowered the ability of neratinib to reduce ERBB1 and K-RAS expression, and to cause tumor cell death. Knock down of ATM-AMPK suppressed vesicle formation and knock down of cathepsin B-AIF significantly reduced neratinib lethality. PKG phosphorylates K-RAS and HMG CoA reductase inhibitors reduce K-RAS farnesylation both of which remove K-RAS from the plasma membrane, abolishing its activity. Neratinib interacted with the PKG activator sildenafil and the HMG CoA reductase inhibitor atorvastatin to further reduce K-RAS expression, and to further enhance cell killing. Neratinib is also a Ste20 kinase family inhibitor and in carcinoma cells, and hematopoietic cancer cells lacking ERBB1/2/4, it reduced K-RAS expression and the phosphorylation of MST1/3/4/Ezrin by ~ 30%. Neratinib increased LATS1 phosphorylation as well as that of YAP and TAZ also by ~ 30%, caused the majority of YAP to translocate into the cytosol and reduced YAP/TAZ protein levels. Neratinib lethality was enhanced by knock down of YAP. Neratinib, in a Rubicon-dependent fashion, reduced PAK1 phosphorylation and that of its substrate Merlin. Our data demonstrate that neratinib coordinately suppresses both mutant K-RAS and YAP function to kill pancreatic tumor cells.
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30
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Aschard H, Laville V, Tchetgen ET, Knights D, Imhann F, Seksik P, Zaitlen N, Silverberg MS, Cosnes J, Weersma RK, Xavier R, Beaugerie L, Skurnik D, Sokol H. Genetic effects on the commensal microbiota in inflammatory bowel disease patients. PLoS Genet 2019; 15:e1008018. [PMID: 30849075 PMCID: PMC6426259 DOI: 10.1371/journal.pgen.1008018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/20/2019] [Accepted: 02/13/2019] [Indexed: 12/16/2022] Open
Abstract
Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease (IBD), and dozens of IBD genetic variants have been identified in genome-wide association studies. However, the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility remains unclear. Here, we studied the association between four major genetic variants associated with an increased risk of IBD and bacterial taxa in up to 633 IBD cases. We performed systematic screening for associations, identifying and replicating associations between NOD2 variants and two taxa: the Roseburia genus and the Faecalibacterium prausnitzii species. By exploring the overall association patterns between genes and bacteria, we found that IBD risk alleles were significantly enriched for associations concordant with bacteria-IBD associations. To understand the significance of this pattern in terms of the study design and known effects from the literature, we used counterfactual principles to assess the fitness of a few parsimonious gene-bacteria-IBD causal models. Our analyses showed evidence that the disease risk of these genetic variants were likely to be partially mediated by the microbiome. We confirmed these results in extensive simulation studies and sensitivity analyses using the association between NOD2 and F. prausnitzii as a case study.
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Affiliation(s)
- Hugues Aschard
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (HA); (DS); (HS)
| | - Vincent Laville
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | - Eric Tchetgen Tchetgen
- Department of Statistics, The Wharton School at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark S. Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ramnik Xavier
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
| | - David Skurnik
- Division of Infectious Diseases, Harvard Medical School, Boston, Massachusetts, United States of America
- Massachusetts Technology and Analytics, Brookline, Massachusetts, United States of America
- Department of Microbiology, Necker Hospital and University Paris Descartes, Paris, France
- INSERM U1151-Equipe 11, Institut Necker-Enfants Malades, Paris, France
- * E-mail: (HA); (DS); (HS)
| | - Harry Sokol
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France
- Sorbonne Université, Paris, France
- Micalis Institute, AgroParisTech, Jouy-en-Josas, France
- INSERM CRSA UMRS U938, Paris, France
- * E-mail: (HA); (DS); (HS)
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King SJ, McCole DF. Epithelial-microbial diplomacy: escalating border tensions drive inflammation in inflammatory bowel disease. Intest Res 2019; 17:177-191. [PMID: 30836737 PMCID: PMC6505084 DOI: 10.5217/ir.2018.00170] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic conditions of the gastrointestinal tract-the main site of host-microbial interaction in the body. Development of IBD is not due to a single event but rather is a multifactorial process where a patient’s genetic background, behavioral habits, and environmental exposures contribute to disease pathogenesis. IBD patients exhibit alterations to gut bacterial populations “dysbiosis” due to the inflammatory microenvironment, however whether this alteration of the gut microbiota precedes inflammation has not been confirmed. Emerging evidence has highlighted the important role of gut microbes in developing measured immune responses and modulating other host responses such as metabolism. Much of the work on the gut microbiota has been correlative and there is an increasing need to understand the intimate relationship between host and microbe. In this review, we highlight how commensal and pathogenic bacteria interact with host intestinal epithelial cells and explore how altered microenvironments impact these connections.
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Affiliation(s)
- Stephanie J King
- Division of Biomedical Sciences, University of California, Riverside, CA, USA
| | - Declan F McCole
- Division of Biomedical Sciences, University of California, Riverside, CA, USA
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SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects. PLoS One 2019; 14:e0211328. [PMID: 30703110 PMCID: PMC6354981 DOI: 10.1371/journal.pone.0211328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Gene-microbiome interactions are important in aetiology and pathogenesis of inflammatory bowel disease, a chronic inflammatory disorder of the gastrointestinal tract consisting of Crohn's disease and ulcerative colitis. Scarce studies on gene-microbiome interactions show very little overlap in their results. Therefore, it is of utmost importance that gene-microbiome studies are repeated. We aimed to replicate the association between the SLC39A8 [Thr]391 risk allele and gut microbiome composition in patients with inflammatory bowel disease and healthy controls. METHODS We collected faecal samples, peripheral blood and extensive phenotype data from 291 patients with inflammatory bowel disease and 476 healthy controls. Carrier status information was obtained from whole exome sequencing data, generated using the Illumina HiSeq. The gut microbiome composition was determined by tag-sequencing the 16S rRNA gene. Associations between carrier status and disease were tested using the Wilcoxon-Mann-Whitney test. Associations between carriers and gut microbiome composition were determined using principal coordinate analyses, variance explained, alpha diversity and additive general linear models in inflammatory bowel disease, healthy controls and all groups combined. RESULTS Crohn's disease patients were more often carriers of the missense variant (21/171, 12.3%) than controls (30/476, 6.3%) (OR = 2.1, P = 0.01). We could not identify associations between carrier status and overall gut microbiome composition and microbial richness in all tested groups after correcting for potential confounding factors. We did identify 37 different operational taxonomical units to be associated with carrier status among the tested groups. Two of these 37 were identified before in the discovery study. CONCLUSIONS We could confirm the genetic association of the SLC39A8 [Thr]391 risk allele with Crohn's disease but we could only limited replicate the association in gut microbiome composition. Independent replication of gene-microbiome studies is warranted to identify true biological mechanisms.
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Yu LCH. Microbiota dysbiosis and barrier dysfunction in inflammatory bowel disease and colorectal cancers: exploring a common ground hypothesis. J Biomed Sci 2018; 25:79. [PMID: 30413188 PMCID: PMC6234774 DOI: 10.1186/s12929-018-0483-8] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease which arises as a result of the interaction of genetic, environmental, barrier and microbial factors leading to chronic inflammation in the intestine. Patients with IBD had a higher risk of developing colorectal carcinoma (CRC), of which the subset was classified as colitis-associated cancers. Genetic polymorphism of innate immune receptors had long been considered a major risk factor for IBD, and the mutations were also recently observed in CRC. Altered microbial composition (termed microbiota dybiosis) and dysfunctional gut barrier manifested by epithelial hyperpermeability and high amount of mucosa-associated bacteria were observed in IBD and CRC patients. The findings suggested that aberrant immune responses to penetrating commensal microbes may play key roles in fueling disease progression. Accumulative evidence demonstrated that mucosa-associated bacteria harbored colitogenic and protumoral properties in experimental models, supporting an active role of bacteria as pathobionts (commensal-derived opportunistic pathogens). Nevertheless, the host factors involved in bacterial dysbiosis and conversion mechanisms from lumen-dwelling commensals to mucosal pathobionts remain unclear. Based on the observation of gut leakiness in patients and the evidence of epithelial hyperpermeability prior to the onset of mucosal histopathology in colitic animals, it was postulated that the epithelial barrier dysfunction associated with mucosal enrichment of specific bacterial strains may predispose the shift to disease-associated microbiota. The speculation of leaky gut as an initiating factor for microbiota dysbiosis that eventually led to pathological consequences was proposed as the "common ground hypothesis", which will be highlighted in this review. Overall, the understanding of the core interplay between gut microbiota and epithelial barriers at early subclinical phases will shed light to novel therapeutic strategies to manage chronic inflammatory disorders and colitis-associated cancers.
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Affiliation(s)
- Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Suite 1020, #1 Jen-Ai Rd. Sec. 1, Taipei, 100, Taiwan, Republic of China.
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Bretin A, Lucas C, Larabi A, Dalmasso G, Billard E, Barnich N, Bonnet R, Nguyen HTT. AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation. Sci Rep 2018; 8:12301. [PMID: 30120269 PMCID: PMC6098085 DOI: 10.1038/s41598-018-30055-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/21/2018] [Indexed: 12/12/2022] Open
Abstract
A high prevalence of adherent-invasive E. coli (AIEC) in the intestinal mucosa of Crohn's disease patients has been shown. AIEC colonize the intestine and induce inflammation in genetically predisposed mouse models including CEABAC10 transgenic (Tg) mice expressing human CEACAM6-receptor for AIEC and eif2ak4-/- mice exhibiting autophagy defect in response to AIEC infection. Here, we aimed at investigating whether gut microbiota modification contributes to AIEC-induced intestinal inflammation in these mouse models. For this, eif2ak4+/+ and eif2ak4-/- mice or CEABAC10 Tg mice invalidated for Eif2ak4 gene (Tg/eif2ak4-/-) or not (Tg/eif2ak4+/+) were infected with the AIEC reference strain LF82 or the non-pathogenic E. coli K12 MG1655 strain. In all mouse groups, LF82 colonized the gut better and longer than MG1655. No difference in fecal microbiota composition was observed in eif2ak4+/+ and eif2ak4-/- mice before infection and at day 1 and 4 post-infection. LF82-infected eif2ak4-/- mice exhibited altered fecal microbiota composition at day 14 and 21 post-infection and increased fecal lipocalin-2 level at day 21 post-infection compared to other groups, indicating that intestinal inflammation developed after microbiota modification. Similar results were obtained for LF82-infected Tg/eif2ak4-/- mice. These results suggest that in genetically predisposed hosts, AIEC colonization might induce chronic intestinal inflammation by altering the gut microbiota composition.
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Affiliation(s)
- Alexis Bretin
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Cécily Lucas
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Anaïs Larabi
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Guillaume Dalmasso
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Elisabeth Billard
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Nicolas Barnich
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
| | - Richard Bonnet
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France
- Centre Hospitalier Universitaire (CHU), Clermont-Ferrand, 63001, France
| | - Hang Thi Thu Nguyen
- M2iSH (Microbes, intestine, inflammation and Susceptibility of the Host), UMR 1071 Inserm, Université Clermont Auvergne, INRA USC 2018, Clermont-Ferrand, 63001, France.
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35
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Abstract
The biological functions of 1α,25-dihydroxyvitamin D3 are regulated by nuclear receptor vitamin D receptor (VDR). The expression level of VDR is high in intestine. VDR is an essential regulator of intestinal cell proliferation, barrier function, and immunity. Vitamin D/VDR plays a protective role in inflammatory bowel diseases (IBDs), both ulcerative colitis and Crohn's disease. Emerging evidence demonstrates low VDR expression and dysfunction of vitamin D/VDR signaling in patients with IBD. Here, we summarize the progress made in vitamin D/VDR signaling in genetic regulation, immunity, and the microbiome in IBD. We cover the mechanisms of intestinal VDR in regulating inflammation through inhibiting the NF-ĸB pathway and activating autophagy. Recent studies suggest that the association of VDR single nucleotide polymorphisms with immune and intestinal pathology may be sex dependent. We emphasize the tissue specificity of VDR and its sex- and time-dependent effects. Furthermore, we discuss potential clinical application and future direction of vitamin D/VDR in preventing and treating IBD.
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Affiliation(s)
- Danika Bakke
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois,Address correspondence to: Jun Sun, PhD, Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, 840 S. Wood Street, Room 704 CSB, MC716, Chicago, IL 60612 ()
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36
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Abstract
Defining the etiology of inflammatory bowel disease (IBD) continues to elude researchers, in part due to the possibility that there may be different triggers for a spectrum of disease phenotypes that are currently classified as either Crohn's disease (CD) or ulcerative colitis (UC). What is clear is that genetic susceptibility plays an important role in the development of IBD, and large genome-wide association studies using case-control approaches have identified more than 230 risk alleles. Many of these identified risk alleles are located in a variety of genes important in host-microbiome interactions. In spite of these major advances, the mechanisms behind the genetic influence on disease development remain unknown. In addition, the identified genetic risks have thus far failed to fully define the hereditability of IBD. Host genetics influence host interactions with the gut microbiota in maintaining health through a balance of regulated immune responses and coordinated microbial composition and function. What remains to be defined is how alterations in these interactions can lead to disease. The nature and cause of changes in the microbiota in patients with IBD are poorly understood. In spite of the large catalog of alterations in the microbiota of IBD patients, inflammation itself can alter the microbiota, leaving open the question of which is cause or effect. The composition and function of the gut microbiota are influenced by many factors, including environmental factors, dietary factors, and, as recent studies have shown, host genetic makeup. More than 200 loci have shown potential to influence the microbiota, but replication and larger studies are still required to validate these findings. It would seem reasonable to consider the combination of both host genetic makeup and the inheritance of the microbiota as interdependent heritable forces that could explain the nature of an individual's susceptibility to IBD or indeed the actual cause of IBD. In this review, we will consider the contribution of the host genetics, the microbiome, and the influence of host genetics on the microbiota to the heritability of IBD.
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Affiliation(s)
- Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ashleigh Goethel
- Department of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Larbi Bedrani
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth Croitoru, MDCM
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
- Correspondence: Kenneth Croitoru, Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Department of Medicine and Immunology, University of Toronto, Mount Sinai Hospital, 600 University Avenue Room 437, Toronto, Ontario, M5G 1X5, Canada ()
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37
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Wang J, Chen L, Zhao N, Xu X, Xu Y, Zhu B. Of genes and microbes: solving the intricacies in host genomes. Protein Cell 2018; 9:446-461. [PMID: 29611114 PMCID: PMC5960464 DOI: 10.1007/s13238-018-0532-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/28/2018] [Indexed: 12/14/2022] Open
Abstract
Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Xizhan Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yakun Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.
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38
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Abstract
Impaired Paneth cell expression of antimicrobial protein (AMP) lysozyme is found in patients with Crohn's disease with the autophagy gene ATG16L1 risk allele, in mice with mutations in autophagy genes Atg16L1, Atg5 and Atg7, and in Irgm1 knockout mice. Defective autophagy is also associated with expansion of resident Gram-negative bacteria in the intestinal lumen. These findings suggest that autophagy may control extracellular resident microbes by governing expression of lysozyme. To test the hypothesis that autophagy may have a defensive role in host response to resident extracellular microbes, we investigated the relationship between gut microbes, autophagy, and lysozyme. RAW 264.7 macrophages were treated with fecal slurry (FS), representing the resident microbial community; lipopolysaccharide (LPS); or butyrate, representing microbial products; or a representative resident Gram-negative bacterium Desulfovibrio vulgaris (DSV). FS, LPS, and DSV inhibited lysozyme expression, whereas butyrate had no effect. Induction of autophagy by rapamycin countered this inhibition, whereas silencing of the autophagy gene Irgm1 exacerbated the inhibitory effects of LPS on lysozyme expression. LPS also inhibited lysozyme activity against DSV and autophagy reversed this effect. Our results provide a novel insight into an interaction between gut bacteria, autophagy and AMP whereby autophagy may defend the host by countering the suppression of antimicrobial protein by Gram-negative bacteria.
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Affiliation(s)
- Sudha B Singh
- 1 Section of Gastroenterology, Medicine Service, New Mexico VA Health Care System, Albuquerque, NM, USA.,2 Division of Gastroenterology and Hepatology, Department of Medicine, the University of New Mexico, Albuquerque, NM, USA
| | - Henry C Lin
- 1 Section of Gastroenterology, Medicine Service, New Mexico VA Health Care System, Albuquerque, NM, USA.,2 Division of Gastroenterology and Hepatology, Department of Medicine, the University of New Mexico, Albuquerque, NM, USA
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39
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Mohammadi A, Kelly OB, Filice M, Kabakchiev B, Smith MI, Silverberg MS. Differential Expression of microRNAs in Peripheral Blood Mononuclear Cells Identifies Autophagy and TGF-Beta-Related Signatures Aberrantly Expressed in Inflammatory Bowel Disease. J Crohns Colitis 2018; 12:568-581. [PMID: 29420705 PMCID: PMC6018685 DOI: 10.1093/ecco-jcc/jjy010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS MicroRNAs [miRNAs] have emerged as important regulators in inflammatory bowel disease [IBD]. This study investigated differential expression of miRNAs across clinical phenotypes in a well-characterized cohort of IBD patients and healthy controls [HCs]. METHODS A cohort of Crohn's disease [CD] and ulcerative colitis [UC] patients and HCs was prospectively accrued. Total RNA was extracted from peripheral blood mononuclear cells for all subjects. miRNA expression was measured using NanoString technologies. The subjects were stratified according to disease activity and location. Statistical significance was assessed per miRNA across outcomes and corrected for multiple testing. miRNA regulation of transcription of important results was confirmed in vitro by a dual luciferase reporter assay and autophagy function was evaluated using immunofluorescence imaging of LC3 puncta in HeLa cells. RESULTS In total, 120 subjects were enrolled. Seventy-four miRNAs were differentially expressed across CD, UC and HCs. Comparing quiescent CD [CDq] with HCs we found ten miRNAs upregulated in CDq. When comparing colonic CD [CCD] to UC, seven miRNAs were upregulated in CCD. The most differentially expressed miRNA in CCD vs UC was miR-874-3p, and we showed its possible utility as a biomarker of differential diagnosis. We showed miR-874-3p targets ATG16L1 and reduces its expression in vitro. An miR-874-3p mimic dysregulates autophagy by a reduction of LC3 in vitro. CONCLUSIONS We identified unique miRNA signatures expressed in distinct IBD phenotypes. These associations highlight pathways dysregulated by aberrant miRNA expression, revealing possible mechanisms underlying the pathophysiology of IBD, but also suggest a cluster of miRNAs as readily accessible biomarkers to aid in differential diagnosis.
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Affiliation(s)
- Aylia Mohammadi
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
| | - Orlaith B Kelly
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada,Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Melissa Filice
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
| | - Boyko Kabakchiev
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
| | - Michelle I Smith
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, ON, Canada,Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, ON, Canada,Corresponding author: Mark Silverberg, 441-600 University Avenue, Toronto, Ontario M5G1X5, Canada. Tel: 1-416-586-4800 ext. 8236; Fax: 1-416-619-5524;
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40
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Lin XT, Zheng XB, Fan DJ, Yao QQ, Hu JC, Lian L, Wu XJ, Lan P, He XS. MicroRNA-143 Targets ATG2B to Inhibit Autophagy and Increase Inflammatory Responses in Crohn's Disease. Inflamm Bowel Dis 2018; 24:781-791. [PMID: 29562274 DOI: 10.1093/ibd/izx075] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Dysfunctional autophagy is recognized as a contributing factor in many chronic inflammatory diseases, including Crohn's disease (CD). Genetic analyses have found that microRNA (miRNA) levels are altered in the intestinal tissues of CD patients. METHODS The Sequencing Alternative Poly-Adenylation Sites (SAPAS) method was used to compare the 3' end of the total mRNA sequence of 3 surgical specimens of CD patients (including inflamed tissues and corresponding noninflamed tissues in each case). The levels of autophagy-related 2B (ATG2B), LC3, and miR-143 were compared between inflamed tissues and noninflamed tissues using immunoblot and quantitative reverse transcription polymerase chain reaction. Luciferase assays were used to verify the interactions between miR-143 and ATG2B. Autophagy was measured by immunoblot analyses of LC3 and transmission electron microscopy. Inflammatory cytokines and IκBα were analyzed to evaluate the effect of miR-143 on inflammatory response. RESULTS The tandem repeat 3'-UTR of ATG2B was longer in inflamed tissues than in corresponding noninflamed tissues and contained an miR-143 target site. miR-143 expression was elevated, whereas ATG2B and LC3-II were downregulated in inflamed tissues. The direct interaction between miR-143 and ATG2B was verified by a 3'-UTR dual-luciferase reporter assay. Constitutive expression of miR-143 or depletion of ATG2B in cultured intestinal epithelial cells inhibited autophagy, reduced IκBα levels, and increased inflammatory responses. CONCLUSIONS miR-143 may induce bowel inflammation by regulating ATG2B and autophagy, suggesting that miR-143 might play a critical role in the development of CD. Therefore, miR-143 could be a promising novel target for gene therapy in CD patients.
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Affiliation(s)
- Xu-Tao Lin
- Department of Gastrointestinal Endoscopy, Guangzhou, Guangdong, China.,Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Bin Zheng
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - De-Jun Fan
- Department of Gastrointestinal Endoscopy, Guangzhou, Guangdong, China.,Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiu-Qiong Yao
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jian-Cong Hu
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Lian
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ping Lan
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Sheng He
- Department of Colorectal Surgery, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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41
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Abstract
The discovery of numerous genetic variants in the human genome that are associated with inflammatory bowel disease (IBD) has revealed critical pathways that play important roles in intestinal homeostasis. These genetic studies have identified a critical role for macroautophagy/autophagy and more recently, lysosomal function, in maintaining the intestinal barrier and mucosal homeostasis. This review highlights recent work on the functional characterization of IBD-associated human genetic variants in cell type-specific functions for autophagy.
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Affiliation(s)
- Kara G Lassen
- a Broad Institute ; Cambridge , MA USA.,b Center for Computational and Integrative Biology ; Massachusetts General Hospital ; Boston , MA USA
| | - Ramnik J Xavier
- a Broad Institute ; Cambridge , MA USA.,b Center for Computational and Integrative Biology ; Massachusetts General Hospital ; Boston , MA USA.,c Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease ; Massachusetts General Hospital; Harvard Medical School ; Boston , MA USA
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42
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Lopes F, Keita ÅV, Saxena A, Reyes JL, Mancini NL, Al Rajabi A, Wang A, Baggio CH, Dicay M, van Dalen R, Ahn Y, Carneiro MBH, Peters NC, Rho JM, MacNaughton WK, Girardin SE, Jijon H, Philpott DJ, Söderholm JD, McKay DM. ER-stress mobilization of death-associated protein kinase-1-dependent xenophagy counteracts mitochondria stress-induced epithelial barrier dysfunction. J Biol Chem 2018; 293:3073-3087. [PMID: 29317503 DOI: 10.1074/jbc.ra117.000809] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
The gut microbiome contributes to inflammatory bowel disease (IBD), in which bacteria can be present within the epithelium. Epithelial barrier function is decreased in IBD, and dysfunctional epithelial mitochondria and endoplasmic reticulum (ER) stress have been individually associated with IBD. We therefore hypothesized that the combination of ER and mitochondrial stresses significantly disrupt epithelial barrier function. Here, we treated human colonic biopsies, epithelial colonoids, and epithelial cells with an uncoupler of oxidative phosphorylation, dinitrophenol (DNP), with or without the ER stressor tunicamycin and assessed epithelial barrier function by monitoring internalization and translocation of commensal bacteria. We also examined barrier function and colitis in mice exposed to dextran sodium sulfate (DSS) or DNP and co-treated with DAPK6, an inhibitor of death-associated protein kinase 1 (DAPK1). Contrary to our hypothesis, induction of ER stress (i.e. the unfolded protein response) protected against decreased barrier function caused by the disruption of mitochondrial function. ER stress did not prevent DNP-driven uptake of bacteria; rather, specific mobilization of the ATF6 arm of ER stress and recruitment of DAPK1 resulted in enhanced autophagic killing (xenophagy) of bacteria. Of note, epithelia with a Crohn's disease-susceptibility mutation in the autophagy gene ATG16L1 exhibited less xenophagy. Systemic delivery of the DAPK1 inhibitor DAPK6 increased bacterial translocation in DSS- or DNP-treated mice. We conclude that promoting ER stress-ATF6-DAPK1 signaling in transporting enterocytes counters the transcellular passage of bacteria evoked by dysfunctional mitochondria, thereby reducing the potential for metabolic stress to reactivate or perpetuate inflammation.
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Affiliation(s)
- Fernando Lopes
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Åsa V Keita
- the Department of Clinical and Experimental Medicine, Division of Surgery, Linköping University, Linköping 581 83, Sweden, and
| | - Alpana Saxena
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Jose Luis Reyes
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Nicole L Mancini
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Ala Al Rajabi
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Arthur Wang
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Cristiane H Baggio
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Michael Dicay
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | - Rob van Dalen
- the Departments of Laboratory Medicine and Pathobiology and
| | - Younghee Ahn
- the Departments of Pediatrics, Clinical Neurosciences, and Physiology and Pharmacology and
| | - Matheus B H Carneiro
- the Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Nathan C Peters
- the Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N4N1, Canada
| | - Jong M Rho
- the Departments of Pediatrics, Clinical Neurosciences, and Physiology and Pharmacology and
| | - Wallace K MacNaughton
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
| | | | - Humberto Jijon
- Medicine, Calvin, Joan, and Phoebe Snyder Institute for Chronic Diseases, and
| | - Dana J Philpott
- Immunology, University of Toronto, Toronto, Ontario M5S1A1, Canada
| | - Johan D Söderholm
- the Department of Clinical and Experimental Medicine, Division of Surgery, Linköping University, Linköping 581 83, Sweden, and
| | - Derek M McKay
- From the Gastrointestinal Research Group, Departments of Physiology and Pharmacology and
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43
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Shen T, Li S, Cai LD, Liu JL, Wang CY, Gan WJ, Li XM, Wang JR, Sun LN, Deng M, Liu YH, Li JM. Erbin exerts a protective effect against inflammatory bowel disease by suppressing autophagic cell death. Oncotarget 2018; 9:12035-12049. [PMID: 29552291 PMCID: PMC5844727 DOI: 10.18632/oncotarget.23925] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/16/2017] [Indexed: 12/22/2022] Open
Abstract
The pathogenesis and key functional molecules involved in inflammatory bowel disease (IBD) including Crohn's disease (CD) and ulcerative colitis (UC) remain unclear. Here, we reported that Erbin, a protein required for the polarity of epithelial cells, is conserved across species and highly expressed in the intestinal mucosa in mice and zebrafish. Pathologically, Erbin expression in the intestinal mucosa was significantly decreased in DSS induced acute colitis mice, IL-10 deficient mice and clinical biopsy specimens from patients with ulcerative colitis. Moreover, Erbin deficient mice are more susceptible to experimental colitis, exhibiting more severe intestinal barrier disruption, with increased histological scores and excessive production of proinflammatory cytokines. Mechanistically, Erbin deficiency or knockdown significantly exacerbated activation of autophagic program and autophagic cell death in vivo and in vitro. And, inhibition of autophagy by Chloroquine attenuates excessive inflammatory response in the DSS-induced colitis mouse model of Erbin deletion. Generally, our study uncovers a crucial role of Erbin in autophagic cell death and IBD, giving rise to a new strategy for IBD therapy by inhibiting excessive activation of autophagy and autophagic cell death.
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Affiliation(s)
- Tong Shen
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Shi Li
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Ling-Dong Cai
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Jing-Lin Liu
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Chu-Yi Wang
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Wen-Juan Gan
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Xiu-Ming Li
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Jing-Ru Wang
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Li-Na Sun
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Min Deng
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
| | - Yu-Hong Liu
- Department of Pathology, Baoan Hospital, Southern Medical University, Shenzhen 518101, People's Republic of China
| | - Jian-Ming Li
- Department of Pathology, Soochow University Medical School, Suzhou 215123, People's Republic of China
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44
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Imhann F, Vila AV, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 2018; 67:108-119. [PMID: 27802154 PMCID: PMC5699972 DOI: 10.1136/gutjnl-2016-312135] [Citation(s) in RCA: 488] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/15/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Patients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset and the heterogeneous presentation of IBD. Therefore, we performed a case-control analysis of the gut microbiota, the host genome and the clinical phenotypes of IBD. DESIGN Stool samples, peripheral blood and extensive phenotype data were collected from 313 patients with IBD and 582 truly healthy controls, selected from a population cohort. The gut microbiota composition was assessed by tag-sequencing the 16S rRNA gene. All participants were genotyped. We composed genetic risk scores from 11 functional genetic variants proven to be associated with IBD in genes that are directly involved in the bacterial handling in the gut: NOD2, CARD9, ATG16L1, IRGM and FUT2. RESULTS Strikingly, we observed significant alterations of the gut microbiota of healthy individuals with a high genetic risk for IBD: the IBD genetic risk score was significantly associated with a decrease in the genus Roseburia in healthy controls (false discovery rate 0.017). Moreover, disease location was a major determinant of the gut microbiota: the gut microbiota of patients with colonic Crohn's disease (CD) is different from that of patients with ileal CD, with a decrease in alpha diversity associated to ileal disease (p=3.28×10-13). CONCLUSIONS We show for the first time that genetic risk variants associated with IBD influence the gut microbiota in healthy individuals. Roseburia spp are acetate-to-butyrate converters, and a decrease has already been observed in patients with IBD.
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Affiliation(s)
- Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Dirk Gevers
- Broad Institute of Harvard and MIT, Boston, USA
| | - Marijn C. Visschedijk
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lieke M. Spekhorst
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rudi Alberts
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Hendrik M. van Dullemen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Rinze W.F. Ter Steege
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Curtis Huttenhower
- Broad Institute of Harvard and MIT, Boston, USA,Biostatistics Department, Harvard School of Public Health, Boston, USA
| | - Gerard Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Ramnik J. Xavier
- Broad Institute of Harvard and MIT, Boston, USA,Massachusetts General Hospital, Boston, USA
| | - Eleonora A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rinse K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
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Harkey MA, Villagran AM, Venkataraman GM, Leisenring WM, Hullar MAJ, Torok-Storb BJ. Associations between gastric dilatation-volvulus in Great Danes and specific alleles of the canine immune-system genes DLA88, DRB1, and TLR5. Am J Vet Res 2017; 78:934-945. [PMID: 28738011 DOI: 10.2460/ajvr.78.8.934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific alleles of candidate genes of the major histocompatibility complex (MHC) and innate immune system were associated with gastric dilatation-volvulus (GDV) in Great Danes. ANIMALS 42 healthy Great Danes (control group) and 39 Great Danes with ≥ 1 GDV episode. PROCEDURES Variable regions of the 2 most polymorphic MHC genes (DLA88 and DRB1) were amplified and sequenced from the dogs in each group. Similarly, regions of 3 genes associated with the innate immune system (TLR5, NOD2, and ATG16L1), which have been linked to inflammatory bowel disease, were amplified and sequenced. Alleles were evaluated for associations with GDV, controlling for age and dog family. RESULTS Specific alleles of genes DLA88, DRB1, and TLR5 were significantly associated with GDV. One allele of each gene had an OR > 2 in the unadjusted univariate analyses and retained a hazard ratio > 2 after controlling for temperament, age, and familial association in the multivariate analysis. CONCLUSIONS AND CLINICAL RELEVANCE The 3 GDV-associated alleles identified in this study may serve as diagnostic markers for identification of Great Danes at risk for GDV. Additional research is needed to determine whether other dog breeds have the same genetic associations. These findings also provided a new target for research into the etiology of, and potential treatments for, GDV in dogs.
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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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Autophagy Genes of Host Responds to Disruption of Gut Microbial Community by Antibiotics. Dig Dis Sci 2017; 62:1486-1497. [PMID: 28466260 DOI: 10.1007/s10620-017-4589-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/21/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Defective autophagic machinery, such as that in Crohn's disease patients homozygous for ATG16L1 risk allele, is associated with alteration of resident gut bacterial communities. However, whether or not host autophagy responds to changes in the resident gut microbial community is not known. Here, we investigated the effect of antibiotic-induced disruption of the gut microbiome (dysbiosis) on autophagy gene expression and the expression of antimicrobial peptides/protein (AMP) over time. AIM To test the hypothesis that antibiotic treatment may cause time-dependent changes in gut bacterial density, autophagy genes, and antimicrobial protein/peptide gene expression. METHODS Mice (n = 8 per group) were treated with antibiotic cocktail and sacrificed at different intervals of recovery (days 3, 7, 10, 14, 21, 28, 35, and 42) post-antibiotics. DNA and RNA were extracted from small intestinal tissues. Bacterial density, expression of host autophagy genes, and AMP genes were analyzed by relative quantitative PCR. Fold change difference in comparison with untreated control group was calculated using 2-ΔΔCt method. Statistical analysis was performed using nonparametric Mann-Whitney test. RESULTS Gut bacterial density changed in a time-dependent fashion in response to antibiotic treatment. These changes were concurrent with upregulation of autophagy genes and antimicrobial peptide/protein gene expression. We further showed that an oral gavage of a resident microbe Desulfovibrio, which bloomed in antibiotic-treated animals, induced Atg5 and lysozyme (Lyz) gene expression. CONCLUSION Autophagy genes respond to dysbiosis induced by antibiotics. This response may be a host mechanism to detect and possibly correct dysbiosis by activating antimicrobial peptides/proteins that control the microbial load in the gut.
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Sokol H, Leducq V, Aschard H, Pham HP, Jegou S, Landman C, Cohen D, Liguori G, Bourrier A, Nion-Larmurier I, Cosnes J, Seksik P, Langella P, Skurnik D, Richard ML, Beaugerie L. Fungal microbiota dysbiosis in IBD. Gut 2017; 66:1039-1048. [PMID: 26843508 PMCID: PMC5532459 DOI: 10.1136/gutjnl-2015-310746] [Citation(s) in RCA: 778] [Impact Index Per Article: 111.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. DESIGN Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. RESULTS We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. CONCLUSIONS Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.
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Affiliation(s)
- Harry Sokol
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Valentin Leducq
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Hang-Phuong Pham
- ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France
| | - Sarah Jegou
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Cecilia Landman
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - David Cohen
- Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Giuseppina Liguori
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Anne Bourrier
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Isabelle Nion-Larmurier
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Jacques Cosnes
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Philippe Seksik
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA,Massachusetts Technology and Analytics, Brookline, Massachusetts, USA
| | - Mathias L Richard
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
| | - Laurent Beaugerie
- Department of Gastroenterology, Saint Antoine Hospital, Paris, France,Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
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Association of ATG16L1 gene haplotype with inflammatory bowel disease in Indians. PLoS One 2017; 12:e0178291. [PMID: 28542425 PMCID: PMC5438258 DOI: 10.1371/journal.pone.0178291] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/10/2017] [Indexed: 01/14/2023] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by multigenic inheritance. Defects in autophagy related genes are considered to show genetic heterogeneity between populations. We evaluated the association of several single nucleotide polymorphisms (SNPs) in the autophagy related 16 like 1 (ATG16L1) gene with IBD in Indians. The ATG16L1 gene was genotyped for ten different SNPs using DNA extracted from peripheral blood of 234 patients with Crohn's disease (CD), 249 patients with ulcerative colitis (UC) and 393 healthy controls The SNPs rs2241880, rs4663396, rs3792106, rs10210302, rs3792109, rs2241877, rs6737398, rs11682898, rs4663402 and rs4663421 were genotyped using the Sequenom MassArray platform. PLINK was used for the association analysis and pairwise linkage disequilibrium (LD) values. Haplotype analysis was done using Haploview. All SNPs were in Hardy Weinberg equilibrium in cases and controls. The G allele at rs6737398 exhibited a protective association with both CD and UC. The T allele at rs4663402 and C allele at rs4663421 were positively associated with CD and UC. The T allele at rs2241877 exhibited protective association with UC only. The AA genotype at rs4663402 and the GG genotype at rs4663421 were protectively associated with both CD and UC. Haplotype analysis revealed that all the SNPs in tight LD (D' = 0.76-1.0) and organized in a single haplotype block. Haplotype D was positively associated with IBD (P = 5.8 x 10-6 for CD and 0.002 for UC). SNPs in ATG16L1 were associated with IBD in Indian patients. The relevance to management of individual patients requires further study.
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50
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Trentesaux C, Fraudeau M, Romagnolo B. [Contribution of autophagy to intestinal homeostasis and pathology]. Med Sci (Paris) 2017; 33:290-296. [PMID: 28367816 DOI: 10.1051/medsci/20173303016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intestinal epithelial cells are crucial mediators of intestinal homeostasis. The intestinal epithelium is the largest of the body's mucosal surfaces exposed to the environment. Intestinal homeostasis is essentially based on the maintenance of intestinal epithelial cell integrity, a complex process involving a balance between the intestinal flora, the immune system and the energy expenses linked to metabolism. Autophagy appears to be central to these functions and allows the epithelium to adapt to its environment and different stress situations by participating in antibacterial defense, by controlling the composition of the intestinal flora and the immune response, and by participating in energy homeostasis. Alterations of this protective mechanism are involved in inflammatory bowel diseases and colorectal cancer.
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Affiliation(s)
- Coralie Trentesaux
- Inserm, U1016, Institut Cochin, département développement, reproduction et cancer, équipe oncogenèse des épithéliums digestifs, 24, rue du faubourg Saint-Jacques, 75014 Paris, France - Cnrs, UMR8104, Paris, France - Université Paris Descartes, Sorbonne Paris Cité, France
| | - Marie Fraudeau
- Inserm, U1016, Institut Cochin, département développement, reproduction et cancer, équipe oncogenèse des épithéliums digestifs, 24, rue du faubourg Saint-Jacques, 75014 Paris, France - Cnrs, UMR8104, Paris, France - Université Paris Descartes, Sorbonne Paris Cité, France
| | - Béatrice Romagnolo
- Inserm, U1016, Institut Cochin, département développement, reproduction et cancer, équipe oncogenèse des épithéliums digestifs, 24, rue du faubourg Saint-Jacques, 75014 Paris, France - Cnrs, UMR8104, Paris, France - Université Paris Descartes, Sorbonne Paris Cité, France
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