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Erkert L, Gamez-Belmonte R, Kabisch M, Schödel L, Patankar JV, Gonzalez-Acera M, Mahapatro M, Bao LL, Plattner C, Kühl AA, Shen J, Serneels L, De Strooper B, Neurath MF, Wirtz S, Becker C. Alzheimer's disease-related presenilins are key to intestinal epithelial cell function and gut immune homoeostasis. Gut 2024; 73:1618-1631. [PMID: 38684238 DOI: 10.1136/gutjnl-2023-331622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE Mutations in presenilin genes are the major cause of Alzheimer's disease. However, little is known about their expression and function in the gut. In this study, we identify the presenilins Psen1 and Psen2 as key molecules that maintain intestinal homoeostasis. DESIGN Human inflammatory bowel disease (IBD) and control samples were analysed for Psen1 expression. Newly generated intestinal epithelium-specific Psen1-deficient, Psen2-deficient and inducible Psen1/Psen2 double-deficient mice were used to dissect the functional role of presenilins in intestinal homoeostasis. RESULTS Psen1 expression was regulated in experimental gut inflammation and in patients with IBD. Induced deletion of Psen1 and Psen2 in mice caused rapid weight loss and spontaneous development of intestinal inflammation. Mice exhibited epithelial barrier disruption with bacterial translocation and deregulation of key pathways for nutrient uptake. Wasting disease was independent of gut inflammation and dysbiosis, as depletion of microbiota rescued Psen-deficient animals from spontaneous colitis development but not from weight loss. On a molecular level, intestinal epithelial cells lacking Psen showed impaired Notch signalling and dysregulated epithelial differentiation. CONCLUSION Overall, our study provides evidence that Psen1 and Psen2 are important guardians of intestinal homoeostasis and future targets for barrier-promoting therapeutic strategies in IBD.
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Affiliation(s)
- Lena Erkert
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Reyes Gamez-Belmonte
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Melanie Kabisch
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Lena Schödel
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Jay V Patankar
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Mousumi Mahapatro
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Li-Li Bao
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
| | - Christina Plattner
- Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Anja A Kühl
- iPATH.Berlin, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jie Shen
- Department of Neurology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lutgarde Serneels
- VIB Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
| | - Bart De Strooper
- VIB Center for Brain and Disease Research, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute@UCL, University College London, London, UK
| | - Markus F Neurath
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Stefan Wirtz
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Christoph Becker
- Department of Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen-Nürnberg, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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Feng Y, Pan M, Li R, He W, Chen Y, Xu S, Chen H, Xu H, Lin Y. Recent developments and new directions in the use of natural products for the treatment of inflammatory bowel disease. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155812. [PMID: 38905845 DOI: 10.1016/j.phymed.2024.155812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/13/2024] [Accepted: 06/06/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) represents a significant global health challenge, and there is an urgent need to explore novel therapeutic interventions. Natural products have demonstrated highly promising effectiveness in the treatment of IBD. PURPOSE This study systematically reviews the latest research advancements in leveraging natural products for IBD treatment. METHODS This manuscript strictly adheres to the PRISMA guidelines. Relevant literature on the effects of natural products on IBD was retrieved from the PubMed, Web of Science and Cochrane Library databases using the search terms "natural product," "inflammatory bowel disease," "colitis," "metagenomics", "target identification", "drug delivery systems", "polyphenols," "alkaloids," "terpenoids," and so on. The retrieved data were then systematically summarized and reviewed. RESULTS This review assessed the different effects of various natural products, such as polyphenols, alkaloids, terpenoids, quinones, and others, in the treatment of IBD. While these natural products offer promising avenues for IBD management, they also face challenges in terms of clinical translation and drug discovery. The advent of metagenomics, single-cell sequencing, target identification techniques, drug delivery systems, and other cutting-edge technologies heralds a new era in overcoming these challenges. CONCLUSION This paper provides an overview of current research progress in utilizing natural products for the treatment of IBD, exploring how contemporary technological innovations can aid in discovering and harnessing bioactive natural products for the treatment of IBD.
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Affiliation(s)
- Yaqian Feng
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China
| | - Mengting Pan
- Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China
| | - Ruiqiong Li
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China
| | - Weishen He
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yangyang Chen
- Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China
| | - Shaohua Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Hui Chen
- Department of Gastroenterology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350004, China.
| | - Huilong Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
| | - Yao Lin
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, China.
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3
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Wang J, Mei L, Hao Y, Xu Y, Yang Q, Dai Z, Yang Y, Wu Z, Ji Y. Contemporary Perspectives on the Role of Vitamin D in Enhancing Gut Health and Its Implications for Preventing and Managing Intestinal Diseases. Nutrients 2024; 16:2352. [PMID: 39064795 PMCID: PMC11279818 DOI: 10.3390/nu16142352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Vitamin D, a crucial fat-soluble vitamin, is primarily synthesized in the skin upon exposure to ultraviolet radiation and is widely recognized as a bone-associated hormone. However, recent scientific advancements have unveiled its intricate association with gut health. The intestinal barrier serves as a vital component, safeguarding the intestinal milieu and maintaining overall homeostasis. Deficiencies in vitamin D have been implicated in altering the gut microbiome composition, compromising the integrity of the intestinal mucosal barrier, and predisposing individuals to various intestinal pathologies. Vitamin D exerts its regulatory function by binding to vitamin D receptors (VDR) present in immune cells, thereby modulating the production of pro-inflammatory cytokines and influencing the intestinal barrier function. Notably, numerous studies have reported lower serum vitamin D levels among patients suffering from intestinal diseases, including inflammatory bowel disease, irritable bowel syndrome, and celiac disease, highlighting the growing significance of vitamin D in gut health maintenance. This comprehensive review delves into the latest advancements in understanding the mechanistic role of vitamin D in modulating the gut microbiome and intestinal barrier function, emphasizing its pivotal role in immune regulation. Furthermore, we consolidate and present relevant findings pertaining to the therapeutic potential of vitamin D in the management of intestinal diseases.
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Affiliation(s)
- Jiaxin Wang
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
| | - Lihua Mei
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
| | - Yanling Hao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China;
| | - Yajun Xu
- Department of Nutrition and Food Hygiene, Peking University, Beijing 100083, China;
| | - Qing Yang
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
| | - Zhaolai Dai
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
| | - Ying Yang
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, China;
| | - Yun Ji
- State Key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing 100193, China; (J.W.); (L.M.); (Q.Y.); (Z.D.); (Y.Y.); (Z.W.)
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4
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Bai Z, Hao J, Chen M, Yao K, Zheng L, Liu L, Hu J, Guo K, Lv Y, Li F. Integrating plasma proteomics with genome-wide association data to identify novel drug targets for inflammatory bowel disease. Sci Rep 2024; 14:16251. [PMID: 39009667 PMCID: PMC11250821 DOI: 10.1038/s41598-024-66780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease that includes Crohn's disease (CD) and ulcerative colitis (UC). Although genome-wide association studies (GWASs) have identified many relevant genetic risk loci, the impact of these loci on protein abundance and their potential utility as clinical therapeutic targets remain uncertain. Therefore, this study aimed to investigate the pathogenesis of IBD and identify effective therapeutic targets through a comprehensive and integrated analysis. We systematically integrated GWAS data related to IBD, UC and CD (N = 25,305) by the study of de Lange KM with the human blood proteome (N = 7213) by the Atherosclerosis Risk in Communities (ARIC) study. Proteome-wide association study (PWAS), mendelian randomisation (MR) and Bayesian colocalisation analysis were used to identify proteins contributing to the risk of IBD. Integrative analysis revealed that genetic variations in IBD, UC and CD affected the abundance of five (ERAP2, RIPK2, TALDO1, CADM2 and RHOC), three (VSIR, HGFAC and CADM2) and two (MST1 and FLRT3) cis-regulated plasma proteins, respectively (P < 0.05). Among the proteins identified via Bayesian colocalisation analysis, CADM2 was found to be an important common protein between IBD and UC. A drug and five druggable target genes were identified from DGIdb after Bayesian colocalisation analysis. Our study's findings from genetic and proteomic approaches have identified compelling proteins that may serve as important leads for future functional studies and potential drug targets for IBD (UC and CD).
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Affiliation(s)
- Zhongyuan Bai
- First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Jiawei Hao
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Miaoran Chen
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Kaixin Yao
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Leilei Zheng
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Liu Liu
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Jingxi Hu
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Kaiqing Guo
- Hepatobiliary Pancreatogastric Surgery, Shanxi Province Cancer Hospital, Taiyuan, China.
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
| | - Yongqiang Lv
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
- Department of Scientific Research, Shanxi Province Cancer Hospital, Taiyuan, China.
| | - Feng Li
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
- Central Laboratory, Shanxi Province Cancer Hospital, Taiyuan, China.
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5
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Sandhu G, Agrawal P, Bose S, Thelma BK. Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis. J Biomol Struct Dyn 2024; 42:5912-5930. [PMID: 37378542 DOI: 10.1080/07391102.2023.2229449] [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] [Received: 01/19/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023]
Abstract
Standard force field-based simulations to accomplish structure-based evaluations of lead molecules is a powerful tool. Combining protein fragmentation into tractable sub-systems with continuum solvation method is envisaged to enable quantum mechanics-based electronic structure calculations of macromolecules in their realistic environment. This along with incorporation of many-body polarization effect in molecular dynamics simulations may augment an accurate description of electrostatics of protein-inhibitor systems for effective drug design. Rheumatoid arthritis (RA) is a complex autoimmune disorder plagued by the ceiling effect of current targeted therapies, encouraging identification of new druggable targets and corresponding drug design to tackle the refractory form of disease. In this study, polarization-inclusive force field approach has been used to model protein solvation and ligand binding for 'Mitogen-activated protein kinase' (MAP3K8), a regulatory node of notable pharmacological relevance in RA synovial biology. For MAP3K8 inhibitors belonging to different scaffold series, the calculations illustrated differential electrostatic contribution to their relative binding affinities and successfully explained examples from available structure-activity relationship studies. Results from this study exemplified i) the advantage of this approach in reliably ranking inhibitors having close nanomolar range activities for the same target; and ii) its prospective application in lead molecule identification aiding drug discovery efforts in RA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gurvisha Sandhu
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
| | - Praveen Agrawal
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - Surojit Bose
- LeadInvent Technologies Private Limited, Biotech Centre, University of Delhi South Campus, New Delhi, Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi, India
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6
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Chen Y, Li X, Sun R, Yang F, Tian W, Huang Q. Screening and experimental validation of diagnostic gene in ulcerative colitis with anti-TNF-α therapy. IUBMB Life 2024; 76:451-463. [PMID: 38269750 DOI: 10.1002/iub.2807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
In clinical practice, the diagnosis of ulcerative colitis (UC) mainly relies on a comprehensive analysis of a series of signs and symptoms of patients. The current biomarkers for diagnosis of UC and prognostic prediction of anti-TNF-α therapy are inaccurate. The present study aimed to perform an integrative analysis of gene expression profiles in patients with UC. A total of seven datasets from the GEO database that met our strict inclusion criteria were included. After identifying differentially expressed genes (DEGs) between UC patients and healthy individuals, the diagnostic and prognostic utility of the DEGs were then analyzed via least absolute shrinkage and selection operator and support-vector machine recursive feature elimination. Subgroup analyses of the treated and untreated groups, as well as the treatment-response group and non-response group, were also performed. Furthermore, the relationship between the expressions of UC-related genes and infiltration of immune cells in the course of treatment was also investigated. Immunohistochemical (IHC) assay was used to verify the gene expression in inflamed UC tissues. When considering all the applied methods, DUOX2, PI3, S100P, MMP7, and S100A8 had priority to be defined as the characteristic genes among DEGs. The area under curve (AUC) of the five genes, which were all consistently over-expressed, based on an external validation dataset, were all above 0.94 for UC diagnosis. Four of the five genes (DUOX2, PI3, MMP7, and S100A8) were down-regulated between treatment-responsive and nonresponsive patients. A significant difference was also observed concerning the infiltration of immune cells, including macrophage and neutrophil, between the two groups (treatment responsive and nonresponsive). The changes in the expression of DUOX2 and MMP7 based on the IHC assay were highly consistent with the results obtained in the current study. This confirmed the mild to moderate diagnostic and predictive value of DUOX2 and MMP7 in patients with UC. The conducted analyses showed that the expression profile of the five identified biomarkers accurately detects UC, whereas four of the five genes evidently predicted the response to anti-TNF-α therapy.
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Affiliation(s)
- Yuan Chen
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Xinfang Li
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Ran Sun
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Fan Yang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Weiliang Tian
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Qian Huang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
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7
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Khrom M, Long M, Dube S, Robbins L, Botwin GJ, Yang S, Mengesha E, Li D, Naito T, Bonthala NN, Ha C, Melmed G, Rabizadeh S, Syal G, Vasiliauskas E, Ziring D, Brant SR, Cho J, Duerr RH, Rioux J, Schumm P, Silverberg M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Xavier RJ, Kugathasan S, Hercules D, Targan SR, Sartor RB, Haritunians T, McGovern DPB. Comprehensive Association Analyses of Extraintestinal Manifestations in Inflammatory Bowel Disease. Gastroenterology 2024; 167:315-332. [PMID: 38490347 PMCID: PMC11193636 DOI: 10.1053/j.gastro.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel disease (IBD) frequently develop extraintestinal manifestations (EIMs) that contribute substantially to morbidity. We assembled the largest multicohort data set to date to investigate the clinical, serologic, and genetic factors associated with EIM complications in IBD. METHODS Data were available in 12,083 unrelated European ancestry IBD cases with presence or absence of EIMs (eg, ankylosing spondylitis [ankylosing spondylitis and sacroiliitis], primary sclerosing cholangitis [PSC], peripheral arthritis, and skin and ocular manifestations) across 4 cohorts (Cedars-Sinai Medical Center, National Institute for Diabetes and Digestive and Kidney Diseases IBD Genetics Consortium, Sinai Helmsley Alliance for Research Excellence Consortium, and Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn's Disease cohort). Clinical and serologic parameters were analyzed by means of univariable and multivariable regression analyses using a mixed-effects model. Within-case logistic regression was performed to assess genetic associations. RESULTS Most EIMs occurred more commonly in female subjects (overall EIM: P = 9.0E-05, odds ratio [OR], 1.2; 95% CI, 1.1-1.4), with CD (especially colonic disease location; P = 9.8E-09, OR, 1.7; 95% CI, 1.4-2.0), and in subjects who required surgery (both CD and UC; P = 3.6E-19, OR, 1.7; 95% CI, 1.5-1.9). Smoking increased risk of EIMs except for PSC, where there was a "protective" effect. Multiple serologic associations were observed, including with PSC (anti-nuclear cytoplasmic antibody; IgG and IgA, anti-Saccharomyces cerevisiae antibodies; and anti-flagellin) and any EIM (anti-nuclear cytoplasmic antibody; IgG and IgA, anti-Saccharomyces cerevisiae antibodies; and anti-Pseudomonas fluorescens-associated sequence). We identified genome-wide significant associations within major histocompatibility complex (ankylosing spondylitis and sacroiliitis, P = 1.4E-15; OR, 2.5; 95% CI, 2.0-3.1; PSC, P = 2.7E-10; OR, 2.8; 95% CI, 2.0-3.8; ocular, P = 2E-08, OR, 3.6; 95% CI, 2.3-5.6; and overall EIM, P = 8.4E-09; OR, 2.2; 95% CI, 1.7-2.9) and CPEB4 (skin, P = 2.7E-08; OR, 1.5; 95% CI, 1.3-1.8). Genetic associations implicated tumor necrosis factor, JAK-STAT, and IL6 as potential targets for EIMs. Contrary to previous reports, only 2% of our subjects had multiple EIMs and most co-occurrences were negatively correlated. CONCLUSIONS We have identified demographic, clinical, and genetic associations with EIMs that revealed underlying mechanisms and implicated novel and existing drug targets-important steps toward a more personalized approach to IBD management.
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MESH Headings
- Humans
- Female
- Male
- Adult
- Cholangitis, Sclerosing/immunology
- Cholangitis, Sclerosing/genetics
- Cholangitis, Sclerosing/diagnosis
- Cholangitis, Sclerosing/complications
- Middle Aged
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/diagnosis
- Crohn Disease/immunology
- Crohn Disease/genetics
- Crohn Disease/diagnosis
- Adolescent
- Risk Factors
- Child
- Spondylitis, Ankylosing/genetics
- Spondylitis, Ankylosing/immunology
- Spondylitis, Ankylosing/diagnosis
- Spondylitis, Ankylosing/complications
- Genetic Predisposition to Disease
- Young Adult
- Sex Factors
- Skin Diseases/etiology
- Skin Diseases/immunology
- Skin Diseases/genetics
- Eye Diseases/etiology
- Eye Diseases/immunology
- Eye Diseases/diagnosis
- Eye Diseases/genetics
- Eye Diseases/epidemiology
- Phenotype
- Inflammatory Bowel Diseases/genetics
- Inflammatory Bowel Diseases/immunology
- Inflammatory Bowel Diseases/diagnosis
- Logistic Models
- Aged
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Affiliation(s)
- Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Millie Long
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Lori Robbins
- Palmetto Digestive Health Specialists, Charleston, South Carolina
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Takeo Naito
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Christina Ha
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gil Melmed
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Shervin Rabizadeh
- Department of Pediatrics, Pediatric Inflammatory Bowel Disease Program, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gaurav Syal
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Eric Vasiliauskas
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Ziring
- Inflammatory Bowel Disease Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Judy Cho
- Icahn School of Medicine at Mount Sinai, Dr Henry D. Janowitz Division of Gastroenterology, New York, New York
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John Rioux
- Department of Medicine, Université de Montréal and Research Center, Montreal Heart Institute, Montréal, Québec, Canada
| | - Phil Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Mark Silverberg
- University of Toronto, Samuel Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Bana Jabri
- University of Chicago, Pritzker School of Medicine, Chicago, Illinois
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Subra Kugathasan
- Children's Healthcare of Atlanta Combined Center for Pediatric Inflammatory Bowel Disease, Atlanta, Georgia; Emory School of Medicine, Atlanta, Georgia
| | | | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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8
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Zhu J, Wang H, Aisikaer M, Yisimayili Z, Yang T, Zhou W, Zhao J, Yunusi K, Aximujiang K. L.acidophilus HSCC LA042 and HKL suspension ameliorate DSS-induced ulcerative colitis in mice by improving the intestinal barrier inhibiting the NLRP3 inflammasome and pathogenic bacteria. Heliyon 2024; 10:e33053. [PMID: 39027449 PMCID: PMC11254534 DOI: 10.1016/j.heliyon.2024.e33053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024] Open
Abstract
Ulcerative Colitis(UC) is a chronic intestinal inflammation affecting the intestines, yet its underlying causes remain unclear. In recent decades, the global prevalence of UC has been on the rise, leading to an increasing demand for therapeutic drugs with minimal side effects. Huan Kui Le (HKL), a traditional Chinese medicine compound, has demonstrated promising efficacy when combined with Lactobacillus acidophilus (Lac.) for UC intervention. However, the precise therapeutic mechanism of this combination remains unknown. The study focused on understanding the mechanisms of UC by examining the effects of Lac. and HKL (LH) treatment. The outcomes discovered that the disruption of gut microbiota, triggered by the activation of the NLRP3 inflammasome, plays a crucial role in UC development. This disruption exacerbates UC symptoms by causing disturbances in inflammatory cytokines and mucosal permeability. We investigated the dynamic changes following the application of this treatment using 16S rRNA sequencing, HE, WB, IHC, and ELISA. Compared with the UC group, LH treatment reduced colon pathological injury, improved colon length, and decreased IL-1 β serum levels. Furthermore, it restored the expression of TJs and preserved mucosal barrier integrity. LH treatment also mitigated colon injury by attenuating the expression of pyroptosis-related genes and proteins, such as NLRP3 and Caspase-1. Additionally, LH treatment altered the gut microbiota's microecology, characterized by a reduction in pathogenic bacteria abundance like Escherichia-shigella and an increase in beneficial bacteria abundance like Akkermansia and Erysipelatoclostridium. Overall, our findings indicate that LH therapy may be associated with intestinal barrier repair, inflammasome inhibition, and gut microbiota regulation, suggesting its potential as a UC treatment.
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Affiliation(s)
- Jiwei Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Hanming Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Muaitaer Aisikaer
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | | | - Tongtong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Wenjun Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Jianfeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
| | - Kurexi Yunusi
- Uygur Medical College, Xinjiang Medical University, Urumqi, 830017, China
| | - Kasimujiang Aximujiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Laboratory of Molecular Biology for Endemic Disease, Urumqi, Xinjiang, 830017, China
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9
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Shaw VR, Byun J, Pettit RW, Hou JK, Walsh KM, Han Y, Amos CI. An Atlas Characterizing the Shared Genetic Architecture of Inflammatory Bowel Disease with Clinical and Behavioral Traits. Inflamm Bowel Dis 2024; 30:884-893. [PMID: 37982439 PMCID: PMC11144996 DOI: 10.1093/ibd/izad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 11/21/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) development is a complex, multifactorial process that involves extrinsic and intrinsic factors such as host genetics, the immune system, the gut microbiome, and environmental risks. To help understand the genetic contribution of clinical, behavioral, psychiatric, and diet-related traits, we aim to provide a deep and comprehensive characterization of the shared genetic architecture between IBD and hundreds of potentially related traits. METHODS Utilizing publicly available summary statistics from a previously published IBD genome-wide association study and hundreds of traits from the United Kingdom BioBank (UKBB), we performed linkage disequilibrium score regression (LDSR) analysis to estimate cross-trait genetic correlations between Crohn's disease (CD), ulcerative colitis (UC), and IBD summary statistics with the UKBB traits of interest. RESULTS Nominally significant (P < .05) genetic correlations were observed for 181 traits in overall IBD, 239 traits in CD, and 94 traits in UC. We replicate the known association between smoking behavior and CD/UC, namely that current tobacco smoking has a positive genetic correlation with CD (rg = 0.12, P = 4.2 × 10-4), while "ever smoking" has a negative genetic correlation with UC (rg = -0.07, P = .042). Globally, all 3 strata (IBD, CD, and UC) demonstrated increased genetic correlations for psychiatric-related traits related to anxiety and depression. CONCLUSION The present analysis reveals the shared genetic architecture between multiple traits and IBD, CD, and UC. Understanding the relevance of joint occurrences of IBD with psychiatric diseases may moderate management of these diseases for individuals jointly affected by them.
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Affiliation(s)
- Vikram R Shaw
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jason K Hou
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX, USA
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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10
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Fehily SR, Basnayake C, Wright EK, Yao CK, Godsell J, Gibson PR, Kamm MA. Probiotics: are they beneficial? Intern Med J 2024; 54:861-870. [PMID: 38717051 DOI: 10.1111/imj.16388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 06/18/2024]
Abstract
There are wide-ranging probiotic choices in Australasia. We reviewed the efficacy of probiotics for the management of gastrointestinal (GI) conditions in adults and assessed relevance to clinical practice. The benefits of probiotics were inconsistent, with a strong consensus reached for only a few of the indications. As different species/strains and combinations differ in efficacy, results cannot be extrapolated from one to another. This review endorses specific probiotics for limited indications. Efficacy of most marketed probiotic formulations remains unstudied and unproven, warranting further research.
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Affiliation(s)
- Sasha R Fehily
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Chamara Basnayake
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Emily K Wright
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - C K Yao
- Department of Gastroenterology, Central Clinical School, Monash University and Alfred Health, Melbourne, Victoria, Australia
| | - Jack Godsell
- Department of Clinical Immunology & Allergy, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Peter R Gibson
- Department of Gastroenterology, Central Clinical School, Monash University and Alfred Health, Melbourne, Victoria, Australia
| | - Michael A Kamm
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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11
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Han A, Yang M, Chen B, Cao G, Xu J, Meng T, Liu Y, Wang Z, Zhou Y, Xu N, Han W, Sun H, Mei Q, Zhu L, Xiong M. Microbiome and its relevance to indigenous inflammatory bowel diseases in China. Gene 2024; 909:148257. [PMID: 38367851 DOI: 10.1016/j.gene.2024.148257] [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] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Inflammatory Bowel Disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract with an unknown etiology. Although dysbiosis is implicated in its pathogenesis, deep sequencing and oral microbiota study in Chinese IBD patients is absent. AIM To explore the role of oral / intestinal microbiota in patients with IBD and the potential associations therein. METHODS Clinical data, fecal and saliva samples were harvested from 80 patients with IBD (Crohn's disease, CD, n = 69; Ulcerative colitis, UC, n = 11) and 24 normal controls. Microbiomics (16S rRNA sequencing and 16S rRNA full-length sequencing) were used to detect and analyze the difference between IBD patients and normal control. RESULTS Compared with normal controls, a higher abundance of the intestinal Shigella spp. (Shigella flexneri and Shigella sonnei, which were positively relate to the severity of IBD), lower abundance of intestinal probiotics (Prevotella, Faecalibacterium and Roseburia), and higher abundance of oral Neisseria were present in IBD patients with microbiome. The higher inflammation-related markers, impaired hepatic and renal function, and dyslipidaemia were present in patients with IBD. A higher intake of red meat and increased abundance of Clostridium in the gut were found in CD patients, while the elevated abundance of Ruminococcus in the gut was showed in UC ones. The bacterial composition of saliva and fecal samples was completely different, yet there was some correlation in the distribution of dominant probiotics. CONCLUSION Enteric dysbacteriosis and the infections of pathogenic bacteria (Shigella) may associate with the occurrence or development of IBD.
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Affiliation(s)
- Anqi Han
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Mingya Yang
- Department of Haematology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Bo Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Guodong Cao
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Junrui Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Tao Meng
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Yu Liu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Zhenzhen Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Yangliu Zhou
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Na Xu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Wei Han
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China
| | - Haiyi Sun
- Clinical Medical Collage, Anhui Medical University, Hefei 230020, PR China
| | - Qiao Mei
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China.
| | - Lixin Zhu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China.
| | - Maoming Xiong
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, PR China.
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12
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Wei S, Li M, Wang Q, Zhao Y, Du F, Chen Y, Deng S, Shen J, Wu K, Yang J, Sun Y, Gu L, Li X, Li W, Chen M, Ling X, Yu L, Xiao Z, Dong L, Wu X. Mesenchymal Stromal Cells: New Generation Treatment of Inflammatory Bowel Disease. J Inflamm Res 2024; 17:3307-3334. [PMID: 38800593 PMCID: PMC11128225 DOI: 10.2147/jir.s458103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract, which has a high recurrence rate and is incurable due to a lack of effective treatment. Mesenchymal stromal cells (MSCs) are a class of pluripotent stem cells that have recently received a lot of attention due to their strong self-renewal ability and immunomodulatory effects, and a large number of experimental and clinical models have confirmed the positive therapeutic effect of MSCs on IBD. In preclinical studies, MSC treatment for IBD relies on MSCs paracrine effects, cell-to-cell contact, and its mediated mitochondrial transfer for immune regulation. It also plays a therapeutic role in restoring the intestinal mucosal barrier through the homing effect, regulation of the intestinal microbiome, and repair of intestinal epithelial cells. In the latest clinical trials, the safety and efficacy of MSCs in the treatment of IBD have been confirmed by transfusion of autologous or allogeneic bone marrow, umbilical cord, and adipose MSCs, as well as their derived extracellular vesicles. However, regarding the stable and effective clinical use of MSCs, several concerns emerge, including the cell sources, clinical management (dose, route and frequency of administration, and pretreatment of MSCs) and adverse reactions. This article comprehensively summarizes the effects and mechanisms of MSCs in the treatment of IBD and its advantages over conventional drugs, as well as the latest clinical trial progress of MSCs in the treatment of IBD. The current challenges and future directions are also discussed. This review would add knowledge into the understanding of IBD treatment by applying MSCs.
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Affiliation(s)
- Shulin Wei
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Mingxing Li
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Qin Wang
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Yueshui Zhao
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Fukuan Du
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Yu Chen
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Shuai Deng
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Jing Shen
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Ke Wu
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Jiayue Yang
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Yuhong Sun
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Li Gu
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Xiaobing Li
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Wanping Li
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Meijuan Chen
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Xiao Ling
- Department of Obstetrics, Luzhou Maternal & Child Health Hospital (Luzhou Second People’s Hospital), Luzhou, Sichuan, 646100, People’s Republic of China
| | - Lei Yu
- Department of Obstetrics, Luzhou Maternal & Child Health Hospital (Luzhou Second People’s Hospital), Luzhou, Sichuan, 646100, People’s Republic of China
| | - Zhangang Xiao
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
| | - Lishu Dong
- Department of Obstetrics, Luzhou Maternal & Child Health Hospital (Luzhou Second People’s Hospital), Luzhou, Sichuan, 646100, People’s Republic of China
| | - Xu Wu
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, 646100, People’s Republic of China
- South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, 646100, People’s Republic of China
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13
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Lin Z, Luo W, Zhang K, Dai S. Environmental and Microbial Factors in Inflammatory Bowel Disease Model Establishment: A Review Partly through Mendelian Randomization. Gut Liver 2024; 18:370-390. [PMID: 37814898 PMCID: PMC11096900 DOI: 10.5009/gnl230179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/09/2023] [Accepted: 07/24/2023] [Indexed: 10/11/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex condition resulting from environmental, microbial, immunologic, and genetic factors. With the advancement of Mendelian randomization research in IBD, we have gained new insights into the relationship between these factors and IBD. Many animal models of IBD have been developed using different methods, but few studies have attempted to model IBD by combining environmental factors and microbial factors. In this review, we examine how environmental factors and microbial factors affect the development and progression of IBD, and how they interact with each other and with the intestinal microbiota. We also summarize the current methods for creating animal models of IBD and compare their advantages and disadvantages. Based on the latest findings from Mendelian randomization studies on the role of environmental factors in IBD, we discuss which environmental and microbial factors could be used to construct a more realistic and reliable IBD experimental model. We propose that animal models of IBD should consider both environmental and microbial factors to better mimic human IBD pathogenesis and to reveal the underlying mechanisms of IBD at the immune and genetic levels. We highlight the importance of environmental and microbial factors in IBD pathogenesis and offer new perspectives and suggestions for improving experimental animal modeling. Our goal is to create a model that closely resembles the clinical picture of IBD.
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Affiliation(s)
- Zesheng Lin
- The First Clinical Medical School, Southern Medical University, Guangzhou, China
| | - Wenjing Luo
- The Second Clinical Medical School, Southern Medical University, Guangzhou, China
| | - Kaijun Zhang
- Department of Gastroenterology, Guangdong Provincial Geriatrics Institute, Guangzhou, ChinaNational Key Clinical Specialty, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shixue Dai
- Department of Gastroenterology, Guangdong Provincial Geriatrics Institute, Guangzhou, ChinaNational Key Clinical Specialty, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Gastroenterology, Geriatric Center, National Regional Medical Center, Ganzhou Hospital Affiliated to Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Ganzhou, China
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14
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Plaza J, Mínguez A, Bastida G, Marqués R, Nos P, Poveda JL, Moret-Tatay I. Genetic Variants Associated with Biological Treatment Response in Inflammatory Bowel Disease: A Systematic Review. Int J Mol Sci 2024; 25:3717. [PMID: 38612528 PMCID: PMC11012229 DOI: 10.3390/ijms25073717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract usually characterized by diarrhea, rectal bleeding, and abdominal pain. IBD includes Crohn's disease and ulcerative colitis as the main entities. IBD is a debilitating condition that can lead to life-threatening complications, involving possible malignancy and surgery. The available therapies aim to achieve long-term remission and prevent disease progression. Biologics are bioengineered therapeutic drugs that mainly target proteins. Although they have revolutionized the treatment of IBD, their potential therapeutic benefits are limited due to large interindividual variability in clinical response in terms of efficacy and toxicity, resulting in high rates of long-term therapeutic failure. It is therefore important to find biomarkers that provide tailor-made treatment strategies that allow for patient stratification to maximize treatment benefits and minimize adverse events. Pharmacogenetics has the potential to optimize biologics selection in IBD by identifying genetic variants, specifically single nucleotide polymorphisms (SNPs), which are the underlying factors associated with an individual's drug response. This review analyzes the current knowledge of genetic variants associated with biological agent response (infliximab, adalimumab, ustekinumab, and vedolizumab) in IBD. An online literature search in various databases was conducted. After applying the inclusion and exclusion criteria, 28 reports from the 1685 results were employed for the review. The most significant SNPs potentially useful as predictive biomarkers of treatment response are linked to immunity, cytokine production, and immunorecognition.
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Affiliation(s)
- Javier Plaza
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), 46026 Valencia, Spain; (J.P.); (A.M.)
- Department of Pharmacy and Pharmaceutical Technology and Parasitology, University of Valencia, 46100 Valencia, Spain
| | - Alejandro Mínguez
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), 46026 Valencia, Spain; (J.P.); (A.M.)
- Inflammatory Bowel Disease Unit, Gastroenterology Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; (G.B.); (P.N.)
| | - Guillermo Bastida
- Inflammatory Bowel Disease Unit, Gastroenterology Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; (G.B.); (P.N.)
| | - Remedios Marqués
- Pharmacy Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; (R.M.); (J.L.P.)
| | - Pilar Nos
- Inflammatory Bowel Disease Unit, Gastroenterology Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; (G.B.); (P.N.)
| | - Jose Luis Poveda
- Pharmacy Department, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain; (R.M.); (J.L.P.)
| | - Inés Moret-Tatay
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), 46026 Valencia, Spain; (J.P.); (A.M.)
- General Directorate of Public Health, Council of Healthcare, 46021 Valencia, Spain
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15
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Dolinger M, Torres J, Vermeire S. Crohn's disease. Lancet 2024; 403:1177-1191. [PMID: 38437854 DOI: 10.1016/s0140-6736(23)02586-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/25/2023] [Accepted: 11/17/2023] [Indexed: 03/06/2024]
Abstract
Crohn's disease is a chronic inflammatory disease of the gastrointestinal tract that might lead to progressive bowel damage and disability. The exact cause of Crohn's disease is unknown, but evidence points towards multifactorial events causing dysregulation of the innate immune system in genetically susceptible people. Commonly affecting the terminal ileum and proximal colon, Crohn's disease inflammation is often discontinuous and patchy, segmental, and transmural. Identification of characteristic findings on ileocolonoscopy and histology remains the diagnostic gold standard, but complete assessment involves laboratory abnormalities, including micronutrient deficiencies, cross-sectional imaging to identify transmural disease extent, severity and complications, and a psychosocial assessment. Treatment strategies for patients with Crohn's disease now go beyond achieving clinical remission to include deeper targets of endoscopic healing and consideration of adjunctive histological and transmural targets to alter disease progression potentially further. The use of early effective advanced therapies and development of therapies targeting alternative novel pathways with improved safety profiles have resulted in a new era of healing in Crohn's disease management. Future combination of advanced therapies with diet or other biological drugs and small molecules, together with improvements in tight control monitoring tools and predictive biomarkers might continue to improve outcomes for patients with Crohn's disease.
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Affiliation(s)
- Michael Dolinger
- Division of Paediatric Gastroenterology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital da Luz, Lisbon, Portugal; Hospital Beatriz Ângelo, Loures, Portugal; Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Severine Vermeire
- Department of Gastroenterology and Hepatology, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
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16
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Torres-Huerta A, Ruley-Haase K, Reed T, Boger-May A, Rubadeux D, Mayer L, Rajashekara AM, Hiller M, Frech M, Roncagli C, Pedersen C, Camacho MC, Hollmer L, English L, Kane G, Boone DL. Retinoid orphan receptor gamma t (rorγt) promotes inflammatory eosinophilia but is dispensable for innate immune-mediated colitis. PLoS One 2024; 19:e0300892. [PMID: 38512959 PMCID: PMC10956760 DOI: 10.1371/journal.pone.0300892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Inflammatory bowel diseases (IBD) result from uncontrolled inflammation in the intestinal mucosa leading to damage and loss of function. Both innate and adaptive immunity contribute to the inflammation of IBD and innate and adaptive immune cells reciprocally activate each other in a forward feedback loop. In order to better understand innate immune contributions to IBD, we developed a model of spontaneous 100% penetrant, early onset colitis that occurs in the absence of adaptive immunity by crossing villin-TNFAIP3 mice to RAG1-/- mice (TRAG mice). This model is driven by microbes and features increased levels of innate lymphoid cells in the intestinal mucosa. To investigate the role of type 3 innate lymphoid cells (ILC3) in the innate colitis of TRAG mice, we crossed them to retinoid orphan receptor gamma t deficient (Rorγt-/-) mice. Rorγt-/- x TRAG mice exhibited markedly reduced eosinophilia in the colonic mucosa, but colitis persisted in these mice. Colitis in Rorγt-/- x TRAG mice was characterized by increased infiltration of the intestinal mucosa by neutrophils, inflammatory monocytes, macrophages and other innate cells. RNA and cellular profiles of Rorγt-/- x TRAG mice were consistent with a lack of ILC3 and ILC3 derived cytokines, reduced antimicrobial factors, increased activation oof epithelial repair processes and reduced activation of epithelial cell STAT3. The colitis in Rorγt-/- x TRAG mice was ameliorated by antibiotic treatment indicating that microbes contribute to the ILC3-independent colitis of these mice. Together, these gene expression and cell signaling signatures reflect the double-edged sword of ILC3 in the intestine, inducing both proinflammatory and antimicrobial protective responses. Thus, Rorγt promotes eosinophilia but Rorγt and Rorγt-dependent ILC3 are dispensable for the innate colitis in TRAG mice.
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Affiliation(s)
- Alvaro Torres-Huerta
- Department of Microbiology & Immunology, Indiana University School of Medicine-South Bend, South Bend, IN, United States of America
| | - Katelyn Ruley-Haase
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Theodore Reed
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Antonia Boger-May
- Department of Microbiology & Immunology, Indiana University School of Medicine-South Bend, South Bend, IN, United States of America
| | - Derek Rubadeux
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Lauren Mayer
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | | | - Morgan Hiller
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Madeleine Frech
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Connor Roncagli
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Cameron Pedersen
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Mary Catherine Camacho
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Lauren Hollmer
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Lauren English
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - Grace Kane
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
| | - David L. Boone
- Department of Microbiology & Immunology, Indiana University School of Medicine-South Bend, South Bend, IN, United States of America
- Department of Biology, University of Notre Dame, South Bend, IN, United States of America
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17
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [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] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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18
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James JP, Riis LB, Søkilde R, Malham M, Høgdall E, Langholz E, Nielsen BS. Short noncoding RNAs as predictive biomarkers for the development from inflammatory bowel disease unclassified to Crohn's disease or ulcerative colitis. PLoS One 2024; 19:e0297353. [PMID: 38408066 PMCID: PMC10896517 DOI: 10.1371/journal.pone.0297353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/22/2023] [Indexed: 02/28/2024] Open
Abstract
Numerous pathogenic processes are mediated by short noncoding RNAs (sncRNA). Twenty percent of inflammatory bowel disease (IBD) patients are labelled as IBD unclassified (IBDU) at disease onset. Most IBDU patients are reclassified as Crohn's disease (CD) or ulcerative colitis (UC) within few years. Since the therapeutic methods for CD and UC differ, biomarkers that can forecast the categorization of IBDU into CD or UC are highly desired. Here, we investigated whether sncRNAs can predict CD or UC among IBDU patients. 35 IBDU patients who were initially diagnosed with IBDU were included in this retrospective investigation; of them, 12, 15, and 8 were reclassified into CD (IBDU-CD), UC (IBDU-UC), or remained as IBDU (IBDU-IBDU), respectively. Eight IBD patients, were included as references. SncRNA profiling on RNA from mucosal biopsies were performed using Affymetrix miRNA 4.0 array. Selected probe sets were validated using RT-qPCR. Among all patients and only adults, 306 and 499 probe sets respectively were differentially expressed between IBDU-CD and IBDU-UC. Six of the probe sets were evaluated by RT-qPCR, of which miR-182-5p, miR-451a and ENSG00000239080 (snoU13) together with age and sex resulted in an AUC of 78.6% (95% CI: 60-97) in discriminating IBDU-CD from IBDU-UC. Based on the three sncRNAs profile it is possible to predict if IBDU patients within 3 years will be reclassified as CD or UC. We showed that the expression profile of IBDU patients differ from that of definite CD or UC, suggesting that a subgroup of IBDU patients may compose a third unique IBD subtype.
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Affiliation(s)
- Jaslin P. James
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rolf Søkilde
- Bioneer A/S, Hørsholm, Kogle Allé 2, Hørsholm, Denmark
| | - Mikkel Malham
- The Pediatric Department, Copenhagen University Hospital—Amager and Hvidovre, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Herlev, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ebbe Langholz
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Gastroenheden, Herlev University Hospital, Herlev, Denmark
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19
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Chen J, Huang Y, Chen H, Yang Q, Zheng W, Lin Y, Xue M, Wang C. Identification of a Novel NLRP12 Frameshift Mutation (Val730Glyfs 41) by Whole-Exome Sequencing in Patients with Crohn’s Disease. Hum Mutat 2024; 2024:1-11. [DOI: 10.1155/2024/5573272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
NLRP12 encodes the nucleotide-binding leucine-rich repeat-containing receptor 12 protein and has been linked to familial cold autoinflammatory syndrome 2 (FCAS2). Previous studies have reported that NLRP12 protein can dampen inflammatory responses in DSS-induced mice colitis. To date, only four alterations in the NLRP12 gene have been associated with Crohn’s disease (CD). Here, we reported a novel heterozygous NLRP12 frameshift mutation (c.2188dupG, p.Val730Glyfs41) identified by whole-exome sequencing in the proband with CD. The Sanger sequencing confirmed that his sister and father also carried this NLRP12 mutation, which cosegregated well with the CD phenotype. In silico analysis predicted this mutation to be disease-causing. Patients heterozygous for this mutation exhibited decreased NLRP12 protein levels in the peripheral blood and colon. Functional assays showed that mutant NLRP12 plasmid-transfected HEK293T cells exhibited significantly lower NLRP12 mRNA and protein levels than wild-type plasmid-transfected cells. The nonsense-mediated decay inhibitor NMDI14 significantly increased NLRP12 mRNA and protein levels in mutant plasmid-transfected cells. Overall, our results demonstrated that this heterozygous NLRP12 mutation (c.2188dupG) resulted in decreased NLRP12 expression, which might contribute to the mechanism underlying CD.
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Affiliation(s)
- Jintong Chen
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Yanni Huang
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Huaning Chen
- Department of Rheumatology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Qinyu Yang
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
| | - Weiwei Zheng
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
| | - Yanjun Lin
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
| | - Mengli Xue
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
| | - Chengdang Wang
- Department of Gastroenterology, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Clinical Research Center for Liver and Intestinal Diseases, Fuzhou 350005, China
- Department of Gastroenterology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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20
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Kai N, Qingsong C, Kejia M, Weiwei L, Xing W, Xuejie C, Lixia C, Minzi D, Yuanyuan Y, Xiaoyan W. An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP). Database (Oxford) 2024; 2024:baad097. [PMID: 38227799 DOI: 10.1093/database/baad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.
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Affiliation(s)
- Nie Kai
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | | | - Ma Kejia
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Luo Weiwei
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Wu Xing
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Chen Xuejie
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Cai Lixia
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University Changsha Hunan 410000, China
| | - Deng Minzi
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Yang Yuanyuan
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
| | - Wang Xiaoyan
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha Hunan 410000, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha Hunan 410000, China
- The College of Computer Science in Sichuan University, Chengdu Sichuan 610000, China
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21
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Shan Y, Chen W, Li Y. The role of m 6A RNA methylation in autoimmune diseases: Novel therapeutic opportunities. Genes Dis 2024; 11:252-267. [PMID: 37588214 PMCID: PMC10425809 DOI: 10.1016/j.gendis.2023.02.013] [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: 06/07/2022] [Revised: 08/02/2022] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Abstract
N6-methyladenosine (m6A) modifications, as one of the most common forms of internal RNA chemical modifications in eukaryotic cells, have gained increasing attention in recent years. The m6A RNA modifications exert various crucial roles in various biological processes, such as embryonic development, neurogenesis, circadian rhythms, and tumorigenesis. Recent advances have highlighted that m6A RNA modification plays an important role in immune response, especially in the initiation and progression of autoimmune diseases. In this review, we summarized the regulatory mechanisms of m6A methylation and its biological functions in the immune system and mainly focused on recent progress in research on the potential role of m6A RNA methylation in the pathogenesis of autoimmune diseases, thus providing possible biomarkers and potential targets for the prevention and treatment of autoimmune diseases.
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Affiliation(s)
- Yunan Shan
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250013, China
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
| | - Wei Chen
- Department of Gastroenterology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yanbin Li
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Neuroimmunology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Jinan, Shandong 250013, China
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22
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Ding W, Marx OM, Mankarious MM, Koltun WA, Yochum GS. Disease Severity Impairs Generation of Intestinal Organoid Cultures From Inflammatory Bowel Disease Patients. J Surg Res 2024; 293:187-195. [PMID: 37776721 DOI: 10.1016/j.jss.2023.08.027] [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] [Received: 04/07/2023] [Revised: 08/02/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
INTRODUCTION Chronic inflammation of the intestinal epithelium is an underlying cause of the two main types of inflammatory bowel disease (IBD), ulcerative colitis (UC), and Crohn's disease (CD). Ex vivo organoids derived from the intestinal epithelium are a useful model to study IBD. Whether such cultures can be established from surgically resected diseased IBD intestinal tissues has not been fully explored. In this study, we tested our ability to establish organoids from nondiseased and diseased IBD intestinal tissues. MATERIALS AND METHODS From 12 UC patients (n = 54 tissues) and 20 CD patients (n = 49 tissues), tissues were collected from multiple colonic regions, and for CD, the terminal ileum was also surveyed. Organoids were cultured in Matrigel domes using defined media. In primary tissues, we conducted immunohistochemical analysis for mucin 2 (MUC2) and Alcian blue staining for goblet cells. Organoids were stained for Ki67, E-cadherin, and MUC2. RESULTS For UC, we were highly successful establishing organoids from nondiseased tissue (n = 12 of 13, 92%). This success rates dropped from tissues with mild (n = 6 of 9, 67%), moderate (n = 2 of 9, 22%), or severe disease (n = 1 of 23, 4%). The rates from nondiseased CD tissues were reduced (n = 11 of 23, 48%) in comparison to such tissues from UC patients. In UC, goblet cells and MUC2 were reduced in diseased tissues and these phenotypes were retained in organoids. CONCLUSIONS Organoids can be readily derived from nondiseased surgically resected IBD tissues. While more work is needed to improve their derivation from diseased tissue, our study supports the use of organoids to study IBD pathophysiology.
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Affiliation(s)
- Wei Ding
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Olivia M Marx
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Marc M Mankarious
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Walter A Koltun
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Gregory S Yochum
- Division of Colon & Rectal Surgery, Department of Surgery, Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania; Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania.
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23
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Sosna B, Aebisher D, Myśliwiec A, Dynarowicz K, Bartusik-Aebisher D, Oleś P, Cieślar G, Kawczyk-Krupka A. Selected Cytokines and Metalloproteinases in Inflammatory Bowel Disease. Int J Mol Sci 2023; 25:202. [PMID: 38203373 PMCID: PMC10779120 DOI: 10.3390/ijms25010202] [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] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a collective term for two diseases: ulcerative colitis (UC) and Crohn's disease (CD). There are many factors, e.g., genetic, environmental and immunological, that increase the likelihood of these diseases. Indicators of IBDs include extracellular matrix metalloproteinases (MMPs). The aim of this review is to present data on the role of selected cytokines and metalloproteinases in IBD. In recent years, more and more transcriptomic studies are emerging. These studies are improving the characterization of the cytokine microenvironment inside inflamed tissue. It is observed that the levels of several cytokines are consistently increased in inflamed tissue in IBD, both in UC and CD. This review shows that MMPs play a major role in the pathology of inflammatory processes, cancer, and IBD. IBD-associated inflammation is associated with increased expression of MMPs and reduced ability of tissue inhibitors of metalloproteinases (TIMPs) to inhibit their action. In IBD patients in tissues that are inflamed, MMPs are produced in excess and TIMP activity is not sufficient to block MMPs. This review is based on our personal selection of the literature that was retrieved by a selective search in PubMed using the terms "Inflammatory bowel disease" and "pathogenesis of Inflammatory bowel diseases" that includes systematic reviews, meta-analyses, and clinical trials. The involvement of the immune system in the pathophysiology of IBD is reviewed in terms of the role of the cytokines and metalloproteinases involved.
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Affiliation(s)
- Barbara Sosna
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - David Aebisher
- Department of Photomedicine and Physical Chemistry, Medical College, University of Rzeszów, 35-959 Rzeszów, Poland;
| | - Angelika Myśliwiec
- Center for Innovative Research in Medical and Natural Sciences, Medical College, University of Rzeszów, 35-310 Rzeszów, Poland; (A.M.); (K.D.)
| | - Klaudia Dynarowicz
- Center for Innovative Research in Medical and Natural Sciences, Medical College, University of Rzeszów, 35-310 Rzeszów, Poland; (A.M.); (K.D.)
| | - Dorota Bartusik-Aebisher
- Department of Biochemistry and General Chemistry, Medical College, University of Rzeszów, 35-959 Rzeszów, Poland;
| | - Piotr Oleś
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - Grzegorz Cieślar
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - Aleksandra Kawczyk-Krupka
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
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24
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Kuffa P, Pickard JM, Campbell A, Yamashita M, Schaus SR, Martens EC, Schmidt TM, Inohara N, Núñez G, Caruso R. Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont. Cell Host Microbe 2023; 31:2007-2022.e12. [PMID: 37967555 PMCID: PMC10842462 DOI: 10.1016/j.chom.2023.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Exclusive enteral nutrition (EEN) with fiber-free diets is an effective steroid-sparing treatment to induce clinical remission in children with Crohn's disease (CD). However, the mechanism underlying the beneficial effects of EEN remains obscure. Using a model of microbiota-dependent colitis with the hallmarks of CD, we find that the administration of a fiber-free diet prevents the development of colitis and inhibits intestinal inflammation in colitic animals. Remarkably, fiber-free diet alters the intestinal localization of Mucispirillum schaedleri, a mucus-dwelling pathobiont, which is required for triggering disease. Mechanistically, the absence of dietary fiber reduces nutrient availability and impairs the dissimilatory nitrate reduction to ammonia (DNRA) metabolic pathway of Mucispirillum, leading to its exclusion from the mucus layer and disease remission. Thus, appropriate localization of the specific pathobiont in the mucus layer is critical for disease development, which is disrupted by fiber exclusion. These results suggest strategies to treat CD by targeting the intestinal niche and metabolism of disease-causing microbes.
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Affiliation(s)
- Peter Kuffa
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph M Pickard
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Misa Yamashita
- Department of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi 755-8505, Japan
| | - Sadie R Schaus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Naohiro Inohara
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gabriel Núñez
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Roberta Caruso
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Rimmer P, Iqbal T. Prognostic modelling in IBD. Best Pract Res Clin Gastroenterol 2023; 67:101877. [PMID: 38103929 DOI: 10.1016/j.bpg.2023.101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
In the ideal world prognostication or predicting disease course in any chronic condition would allow the clinician to anticipate disease behaviour, providing crucial information for the patient and data regarding best use of resources. Prognostication also allows an understanding of likely response to treatment and the risk of adverse effects of a treatment leading to withdrawal in any individual patient. Therefore, the ability to predict outcomes from the onset of disease is the key step to developing precision personalised medicine, which is the design of medical care to optimise efficiency or therapeutic benefit based on careful profiling of patients. An important corollary is to prevent unnecessary healthcare costs. This paper outlines currently available predictors of disease outcome in IBD and looks to the future which will involve the use of artificial intelligence to interrogate big data derived from various important 'omes' to tease out a more holistic approach to IBD.
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Affiliation(s)
- Peter Rimmer
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
| | - Tariq Iqbal
- Queen Elizabeth Hospital Birmingham, B15 2TH, UK; University of Birmingham, College of Medical and Dental Science, UK.
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26
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Miller A, Cutroneo G, Lombardo GP, D'Angelo R, Pallio S, Migliorato A, Fumia A, Favaloro A, Lauriano ER, Pergolizzi S. Association between neuropeptides and mucins in Crohn's disease mucous cells. Acta Histochem 2023; 125:152115. [PMID: 37979446 DOI: 10.1016/j.acthis.2023.152115] [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] [Received: 09/23/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023]
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are both inflammatory bowel diseases (IBD). Unlike UC, which is limited to the mucosa of the colon, CD inflammation is characterized by chronic mucosal ulcerations affecting the entire gastrointestinal tract. Goblet cells (GCs) can be found in some lining epithelia, particularly in the respiratory and digestive tracts. GCs represent the main source of mucin that are the significant components of the mucus layer; hypertrophy of GCs and an increase in mucin production are observed in many enteric infections. The cytoplasm of goblet cells may also contain neuropeptides, such as serotonin, that can be altered in inflammatory bowel disease (IBD). The defense system of the gut is represented by the intestinal mucosal barrier, its protective function is strictly connected to the regulation of the mucus layer and the coordination of the neuro-immune response. Paraformaldehyde-fixed intestinal tissues, obtained from fifteen patients with Crohn's disease, were analyzed by immunostaining for MUC2, MUC4, 5-HT, and VAChT. This study aims to define the link between neuropeptides and mucins in mucous cells and their involvement in the inflammation process. Our results showed in mucous cells of Crohn's disease (CD) patients a high expression of MUC4 and a decrease in the expression of vesicular acetylcholine transporter (VAChT) demonstrating the presence of an inflammatory state.
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Affiliation(s)
- Anthea Miller
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Giuseppina Cutroneo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, 98125 Messina, Italy
| | - Giorgia Pia Lombardo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Roberta D'Angelo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Socrate Pallio
- Department of Clinical and Experimental Medicine, University of Messina, 98147 Messina, Italy
| | - Alba Migliorato
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, 98125 Messina, Italy
| | - Angelo Fumia
- Department of Clinical and Experimental Medicine, University of Messina, 98147 Messina, Italy.
| | - Angelo Favaloro
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, 98125 Messina, Italy
| | - Eugenia Rita Lauriano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Simona Pergolizzi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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Do KH, Ko SH, Kim KB, Seo K, Lee WK. Comparative Study of Intestinal Microbiome in Patients with Ulcerative Colitis and Healthy Controls in Korea. Microorganisms 2023; 11:2750. [PMID: 38004761 PMCID: PMC10673479 DOI: 10.3390/microorganisms11112750] [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: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Ulcerative colitis (UC) poses a contemporary medical challenge, with its exact cause still eluding researchers. This is due to various factors, such as the rising incidence, diagnostic complexities, and difficulties associated with its management. We compared the intestinal microbiome of patients with UC to that of healthy controls to determine the qualitative and quantitative changes associated with UC that occur in the intestinal microbiota. The intestinal bacterial abundance in 40 Korean patients with UC and 25 healthy controls was assayed using via next-generation sequencing. There were five major phyla in both groups: Firmicutes (UC patients: 51.12%; healthy controls: 46.90%), Bacteroidota (UC patients: 37.04%; healthy controls: 40.34%), Proteobacteria (UC patients: 6.01%; healthy controls: 11.05%), Actinobacteriota (UC patients: 5.71%; healthy controls: 1.56%), and Desulfobacteriota (UC patients: 0.13%; healthy controls: 0.14%). Firmicutes was more prevalent in patients with UC (51.12%) compared to that of healthy controls (46.90%). Otherwise, Bacteroidota was more prevalent in healthy controls (40.34%) compared to patients with UC (37.04%). Although there was no significant difference, our results showed a substantially lower gut microbiome diversity in patients with UC (mean: 16.5; 95% confidence interval (CI) = 14.956-18.044) than in healthy controls (mean: 17.84; 95% CI = 15.989-19.691), the beta diversity and the flora structure of the microbiome in patients with UC differed from those in healthy controls. This will be helpful for the development of new treatment options and lay the groundwork for future research on UC. To understand the disease mechanism, it is essential to define the different types of microbes in the guts of patients with UC.
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Affiliation(s)
- Kyung-Hyo Do
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea;
| | - Seung-Hyun Ko
- GutBiomeTech Co., Ltd., Cheongju 28644, Republic of Korea
| | - Ki Bae Kim
- Department of Internal Medicine, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
| | - Kwangwon Seo
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea;
| | - Wan-Kyu Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea;
- GutBiomeTech Co., Ltd., Cheongju 28644, Republic of Korea
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29
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Xie W, Jiang H, Chen Y, Zhang H, Song Y, Yu Z, Gu H, Xu H, Han S, Li S, Liu N, Han S. Association between systemic lupus erythematosus and inflammatory bowel disease in European and East Asian populations: a two-sample Mendelian randomization study. Front Immunol 2023; 14:1199896. [PMID: 38022503 PMCID: PMC10654968 DOI: 10.3389/fimmu.2023.1199896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background Previous studies have shown a coexistence phenomenon between systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), but the causal relationship between them is still unclear. Therefore, we conducted a two-sample Mendelian randomization (MR) analysis using publicly available summary statistics data to evaluate whether there was a causal relationship between the two diseases. Methods Summary statistics for SLE and IBD were downloaded from the Open Genome-Wide Association Study and the International Inflammatory Bowel Disease Genetics Consortium. European and East Asian populations were included in this MR work. We adopted a series of methods to select instrumental variables that are closely related to SLE and IBD. To make the conclusion more reliable, we applied a variety of different analysis methods, among which the inverse variance-weighted (IVW) method was the main method. In addition, heterogeneity, pleiotropy, and sensitivity were assessed to make the conclusions more convincing. Results In the European population, a negative causal relationship was observed between SLE and overall IBD (OR = 0.94; 95% CI = 0.90, 0.98; P < 0.004) and ulcerative colitis (UC) (OR = 0.93; 95% CI = 0.88, 0.98; P = 0.006). After removing outliers with Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO), the results remained consistent with IVW. However, there was no causal relationship between SLE and Crohn's disease. In the East Asian population, no causal relationship was found between SLE and IBD. Conclusion Our results found that genetic susceptibility to SLE was associated with lower overall IBD risk and UC risk in European populations. In contrast, no association between SLE and IBD was found in East Asian populations. This work might enrich the previous research results, and it may provide some references for research in the future.
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Affiliation(s)
- Weidong Xie
- Department of The Gastrointestinal Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haojie Jiang
- Department of The Gastrointestinal Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yao Chen
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Graduate School, Zhejiang University, Hangzhou, China
| | | | - Yaoyu Song
- Wenzhou Medical University, Wenzhou, China
| | - Zhaojie Yu
- Wenzhou Medical University, Wenzhou, China
| | - Huayan Gu
- Department of Breast Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hongkai Xu
- Department of The Gastrointestinal Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Saiyi Han
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou people’s Hospital, Quzhou, China
| | - Sen Li
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Naxin Liu
- Department of The Gastrointestinal Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shaoliang Han
- Department of The Gastrointestinal Surgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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30
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Yii CY, Chiu HH, Yong SB. Comment: Polymorphisms indicating risk of inflammatory bowel disease or antigenicity to anti-TNF drugs as biomarkers of response in children. Pharmacol Res 2023; 196:106937. [PMID: 37769888 DOI: 10.1016/j.phrs.2023.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Chin-Yuan Yii
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Landseed International Hospital, Taoyuan, Taiwan; Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Hsien Hung Chiu
- Department of Education, China Medical University Hospital, Taichung, Taiwan
| | - Su-Boon Yong
- Department of Allergy and Immunology, China Medical University Children's, Hospital, Taichung, Taiwan; Department of Medicine, College of Medicine, China Medical University, Taichung, Taiwan; Research Center for Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Hospital, Taichung, Taiwan.
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31
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Lei P, Yu H, Ma J, Du J, Fang Y, Yang Q, Zhang K, Luo L, Jin L, Wu W, Sun D. Cell membrane nanomaterials composed of phospholipids and glycoproteins for drug delivery in inflammatory bowel disease: A review. Int J Biol Macromol 2023; 249:126000. [PMID: 37532186 DOI: 10.1016/j.ijbiomac.2023.126000] [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] [Received: 05/30/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
Inflammatory bowel disease (IBD) is a serious chronic intestinal disorder with an increasing global incidence. However, current treatment strategies, such as anti-inflammatory drugs and probiotics, have limitations in terms of safety, stability, and effectiveness. The emergence of targeted nanoparticles has revolutionized IBD treatment by enhancing the biological properties of drugs and promoting efficiency and safety. Unlike synthetic nanoparticles, cell membrane nanomaterials (CMNs) consist primarily of biological macromolecules, including phospholipids, proteins, and sugars. CMNs include red blood cell membranes, macrophage membranes, and leukocyte membranes, which possess abundant glycoprotein receptors and ligands on their surfaces, allowing for the formation of cell-to-cell connections with other biological macromolecules. Consequently, they exhibit superior cell affinity, evade immune responses, and target inflammation effectively, making them ideal material for targeted delivery of IBD therapies. This review explores various CMNs delivery systems for IBD treatment. However, due to the complexity and harsh nature of the intestinal microenvironment, the lack of flexibility or loss of selectivity poses challenges in designing single CMNs delivery strategies. Therefore, we propose a hierarchically programmed delivery modality that combines CMNs with pH, charge, ROS and ligand-modified responsive nanoparticles. This approach significantly improves delivery efficiency and points the way for future research in this area.
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Affiliation(s)
- Pengyu Lei
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Haiyang Yu
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Jiahui Ma
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Yimeng Fang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China
| | - Qinsi Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Kun Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, China
| | - Li Luo
- Affiliated Dongguan Hospital, Southern Medical University, Dongguan, Guangdong 523059, China
| | - Libo Jin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China.
| | - Wei Wu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, China.
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou 325035, China.
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Yue NN, Xu HM, Xu J, Zhu MZ, Zhang Y, Tian CM, Nie YQ, Yao J, Liang YJ, Li DF, Wang LS. Therapeutic potential of gene therapy for gastrointestinal diseases: Advancements and future perspectives. Mol Ther Oncolytics 2023; 30:193-215. [PMID: 37663132 PMCID: PMC10471515 DOI: 10.1016/j.omto.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023] Open
Abstract
Advancements in understanding the pathogenesis mechanisms underlying gastrointestinal diseases, encompassing inflammatory bowel disease, gastrointestinal cancer, and gastroesophageal reflux disease, have led to the identification of numerous novel therapeutic targets. These discoveries have opened up exciting possibilities for developing gene therapy strategies to treat gastrointestinal diseases. These strategies include gene replacement, gene enhancement, gene overexpression, gene function blocking, and transgenic somatic cell transplantation. In this review, we introduce the important gene therapy targets and targeted delivery systems within the field of gastroenterology. Furthermore, we provide a comprehensive overview of recent progress in gene therapy related to gastrointestinal disorders and shed light on the application of innovative gene-editing technologies in treating these conditions. These developments are fueling a revolution in the management of gastrointestinal diseases. Ultimately, we discuss the current challenges (particularly regarding safety, oral efficacy, and cost) and explore potential future directions for implementing gene therapy in the clinical settings for gastrointestinal diseases.
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Affiliation(s)
- Ning-ning Yue
- Department of Gastroenterology, Shenzhen People’s Hospital (the Second Clinical Medical College, Jinan University), Shenzhen 518000, China
| | - Hao-ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Min-zheng Zhu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, Guangdong 516000, China
| | - Cheng-Mei Tian
- Department of Emergency, Shenzhen People’s Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518000, China
| | - Yu-qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou 510000, China
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518000, China
| | - Yu-jie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen 518000, China
| | - De-feng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518000, China
| | - Li-sheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (the Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518000, China
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Abstract
The gut microbiome is a dense and metabolically active consortium of microorganisms and viruses located in the lower gastrointestinal tract of the human body. Bacteria and their viruses (phages) are the most abundant members of the gut microbiome. Investigating their biology and the interplay between the two is important if we are to understand their roles in human health and disease. In this review, we summarize recent advances in resolving the taxonomic structure and ecological functions of the complex community of phages in the human gut-the gut phageome. We discuss how age, diet, and geography can all have a significant impact on phageome composition. We note that alterations to the gut phageome have been observed in several diseases such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer, and we evaluate whether these phageome changes can directly or indirectly contribute to disease etiology and pathogenesis. We also highlight how lack of standardization in studying the gut phageome has contributed to variation in reported results.
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Affiliation(s)
- Ciara A Tobin
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, Cork, Ireland; , ,
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
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34
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Mankarious MM, Connelly TM, Harris L, Deiling S, Yochum GS, Koltun WA. Creating a Surgical Biobank: The Hershey Medical Center Experience. Dis Colon Rectum 2023; 66:1174-1184. [PMID: 37378558 DOI: 10.1097/dcr.0000000000002944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
BACKGROUND Tissue harvesting at the time of surgery offers surgeons and scientists a unique opportunity to discover and better understand disease pathophysiology. Tissue biobanking presents challenges in patient consents, specimen collection, preparation, and storage, but the potential for scientific discovery justifies the effort. Although the number of tissue biobanks is increasing worldwide, information regarding necessary infrastructure, process flow, and management of expected obstacles is lacking. OBJECTIVE To provide a framework and motivation for clinician scientists intending to start an intestinal tissue biobank under their direction. DATA SOURCES The Carlino Family Inflammatory Bowel and Colorectal Diseases Biobank is housed at the Milton S. Hershey Medical Center. STUDY SELECTION Review. INTERVENTION Implementation of a surgical tissue biobank at a large tertiary care institution. MAIN OUTCOME MEASURES Assess critical challenges and obstacles over the years as well as keys to the success of the program. RESULTS Over 2 decades, the institutional biobank grew from an IBD biobank to one which now incorporates thousands of surgical specimens representing numerous colorectal diseases. This was done through a process of refinement focusing on patient recruitment and an efficient consenting and specimen management process. The biobank's success is further insured by institutional, external, and philanthropic support; scientific collaborations; and sharing of biological specimens with other groups of dedicated researchers. LIMITATIONS This is a single-center experience in collecting surgically resected colorectal specimens. CONCLUSIONS Surgical specimen biobanks are essential in studying disease cause using genomics, transcriptomics, and proteomic technologies. Therefore, surgeons, clinicians, and scientists should build biobanks at their institutions to promote further scientific discovery and improve specimen diversity.
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Affiliation(s)
- Marc M Mankarious
- Division of Colon and Rectal Surgery, Department of Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Tara M Connelly
- Department of Surgery, University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Leonard Harris
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Sue Deiling
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Gregory S Yochum
- Division of Colon and Rectal Surgery, Department of Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Walter A Koltun
- Division of Colon and Rectal Surgery, Department of Surgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania
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Lou Y, Jiang S, Song M, Wang H, Han M, Tian X, Zhao Y, Gao J, Song Y, Ma S, Zhao P, Zheng Q, Niu Z, Zhang W, Chang T, Chen YH, Wang H. Epithelial TIPE1 Protein Guards against Colitis by Inhibiting TNF-α-Mediated Inflammation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:874-884. [PMID: 37459052 DOI: 10.4049/jimmunol.2300291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/28/2023] [Indexed: 08/23/2023]
Abstract
Intestinal epithelial cells (IECs) at the internal/external interface orchestrate the mucosal immune response, and IEC dysfunction has been linked to multiple inflammatory diseases, including inflammatory bowel disease. In this study, we found that a member of the TNF-α-induced protein 8 (TNFAIP8 or TIPE) family called TIPE1 is indispensable for maintaining epithelial cell barrier integrity and homeostasis under inflammatory conditions. TIPE1-deficient mice, or chimeric mice that were deficient in TIPE1 in their nonhematopoietic cells, were more sensitive to dextran sulfate sodium-induced experimental colitis; however, TIPE1 deficiency had no impact on the development of inflammation-associated and sporadic colorectal cancers. Mechanistically, TIPE1 prevented experimental colitis through modulation of TNF-α-dependent inflammatory response in IECs. Importantly, genetic deletion of both TIPE1 and its related protein TNFAIP8 in mice led to the development of spontaneous chronic colitis, indicating that both of these two TIPE family members play crucial roles in maintaining intestinal homeostasis. Collectively, our findings highlight an important mechanism by which TIPE family proteins maintain intestinal homeostasis and prevent inflammatory disorders in the gut.
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Affiliation(s)
- Yunwei Lou
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Shan Jiang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Miaomiao Song
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
| | - Han Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
| | - Meijuan Han
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Xueqin Tian
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Yuxin Zhao
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Morphologic Center of College of Basic Medicine, Xinjiang Medical University, Xinjiang, China
| | - Jingtao Gao
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Morphologic Center of College of Basic Medicine, Xinjiang Medical University, Xinjiang, China
| | - Yaru Song
- Department of Pulmonary Medicine, The Affiliated Renmin Hospital of Xinxiang Medical University, Xinxiang, China
| | - Shujun Ma
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Peiqing Zhao
- Center of Translational Medicine, Zibo Central Hospital, Shandong University, Shandong, China
| | - Qianqian Zheng
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
| | - Zhiyuan Niu
- Synthetic Biology Engineering Lab of Henan Province, School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, China
| | - Wen Zhang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
| | - Tingmin Chang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Youhai H Chen
- School of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wang
- Henan Key Laboratory of Immunology and Targeted Drugs, Xinxiang Medical University, Xinxiang, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, China
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Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD. The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population. Front Immunol 2023; 14:1161901. [PMID: 37600767 PMCID: PMC10436103 DOI: 10.3389/fimmu.2023.1161901] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction The imbalance between Th17 and regulatory T cells in inflammatory bowel diseases (IBD) promotes intestinal epithelial cell damage. In this scenario, T helper cell lineage commitment is accompanied by dynamic changes to the chromatin that facilitate or repress gene expression. Methods Here, we characterized the chromatin landscape and heterogeneity of intestinal and peripheral CD4 T cellsfrom IBD patients using in house ATAC-Seq and single cell RNA-Seq libraries. Results We show that chromatin accessibility profiles of CD4 T cells from inflamed intestinal biopsies relate to genes associated with a network of inflammatory processes. After integrating the chromatin profiles of tissue-derived CD4 T cells and in-vitro polarized CD4 T cell subpopulations, we found that the chromatin accessibility changes of CD4 T cells were associated with a higher predominance of pathogenic Th17 cells (pTh17 cells) in inflamed biopsies. In addition, IBD risk loci in CD4 T cells were colocalized with accessible chromatin changes near pTh17-related genes, as shown in intronic STAT3 and IL23R regions enriched in areas of active intestinal inflammation. Moreover, single cell RNA-Seq analysis revealed a population of pTh17 cells that co-expresses Th1 and cytotoxic transcriptional programs associated with IBD severity. Discussion Altogether, we show that cytotoxic pTh17 cells were specifically associated with IBD genetic variants and linked to intestinal inflammation of IBD patients.
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Affiliation(s)
- Tiago S. Medina
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michelle Smith
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Gabriela S. Kinker
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Ankur Chakravarthy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Williams Turpin
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Helen L. Yau
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Olga F. Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - William Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Mark S. Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Alfonso Perez G, Castillo R. Gene Identification in Inflammatory Bowel Disease via a Machine Learning Approach. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1218. [PMID: 37512030 PMCID: PMC10383667 DOI: 10.3390/medicina59071218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Inflammatory bowel disease (IBD) is an illness with increasing prevalence, particularly in emerging countries, which can have a substantial impact on the quality of life of the patient. The illness is rather heterogeneous with different evolution among patients. A machine learning approach is followed in this paper to identify potential genes that are related to IBD. This is done by following a Monte Carlo simulation approach. In total, 23 different machine learning techniques were tested (in addition to a base level obtained using artificial neural networks). The best model identified 74 genes selected by the algorithm as being potentially involved in IBD. IBD seems to be a polygenic illness, in which environmental factors might play an important role. Following a machine learning approach, it was possible to obtain a classification accuracy of 84.2% differentiating between patients with IBD and control cases in a large cohort of 2490 total cases. The sensitivity and specificity of the model were 82.6% and 84.4%, respectively. It was also possible to distinguish between the two main types of IBD: (1) Crohn's disease and (2) ulcerative colitis.
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Affiliation(s)
- Gerardo Alfonso Perez
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castello, Spain
| | - Raquel Castillo
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castello, Spain
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Kim SM, Park S, Hwang SH, Lee EY, Kim JH, Lee GS, Lee G, Chang DH, Lee JG, Hwang J, Lee Y, Kyung M, Kim EK, Kim JH, Kim TH, Moon JH, Kim BC, Ko G, Kim SY, Ryu JH, Lee JS, Lee CH, Kim JY, Kim S, Lee WJ, Kim MH. Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis. Cell Host Microbe 2023; 31:1021-1037.e10. [PMID: 37269833 DOI: 10.1016/j.chom.2023.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 03/23/2023] [Accepted: 05/09/2023] [Indexed: 06/05/2023]
Abstract
Commensal bacteria are critically involved in the establishment of tolerance against inflammatory challenges, the molecular mechanisms of which are just being uncovered. All kingdoms of life produce aminoacyl-tRNA synthetases (ARSs). Thus far, the non-translational roles of ARSs have largely been reported in eukaryotes. Here, we report that the threonyl-tRNA synthetase (AmTARS) of the gut-associated bacterium Akkermansia muciniphila is secreted and functions to monitor and modulate immune homeostasis. Secreted AmTARS triggers M2 macrophage polarization and orchestrates the production of anti-inflammatory IL-10 via its unique, evolutionary-acquired regions, which mediates specific interactions with TLR2. This interaction activates the MAPK and PI3K/AKT signaling pathways, which converge on CREB, leading to an efficient production of IL-10 and suppression of the central inflammatory mediator NF-κB. AmTARS restores IL-10-positive macrophages, increases IL-10 levels in the serum, and attenuates the pathological effects in colitis mice. Thus, commensal tRNA synthetases can act as intrinsic mediators that maintain homeostasis.
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Affiliation(s)
- Su-Man Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Biology Education, Chonnam National University, Gwangju 61186, Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea
| | - Seung-Ho Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jong-Hwan Kim
- Korean Bioinformation Center, KRIBB, Daejeon 34141, Korea
| | - Ga Seul Lee
- Core Research Facility & Analysis Center, KRIBB, Daejeon 34141, Korea; College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea
| | - Giljae Lee
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea
| | - Dong-Ho Chang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jae-Geun Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Minsoo Kyung
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eun-Kyoung Kim
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae-Hoon Kim
- Laboratory Animal Resource Center, KRIBB, Daejeon 34141, Korea
| | - Tae-Hwan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Korea
| | - Jeong Hee Moon
- Core Research Facility & Analysis Center, KRIBB, Daejeon 34141, Korea
| | - Byoung-Chan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; HealthBiome, Inc., Bioventure Center, Daejeon 34141, Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea; Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul 08826, Korea; KoBioLabs, Inc., Seoul 08826, Korea; Bio-MAX/N-Bio, Seoul National University, Seoul 08826, Korea
| | - Seon-Young Kim
- Korean Bioinformation Center, KRIBB, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong-Soo Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, KRIBB, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong-Yoon Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, College of Pharmacy and College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon 21983, Republic of Korea
| | - Won-Jae Lee
- National Creative Research Initiative Center for Hologenomics and School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
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Mu C, Zhao Q, Zhao Q, Yang L, Pang X, Liu T, Li X, Wang B, Fung SY, Cao H. Multi-omics in Crohn's disease: New insights from inside. Comput Struct Biotechnol J 2023; 21:3054-3072. [PMID: 37273853 PMCID: PMC10238466 DOI: 10.1016/j.csbj.2023.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development of high-throughput sequencing technology with integrated-omics analyses in recent years has provided a new means for exploring the pathogenesis, mining the biomarkers and designing targeted personalized therapeutics of CD. Host genomics and epigenomics unveil heredity-related mechanisms of susceptible individuals, while microbiome and metabolomics map host-microbe interactions in CD patients. Proteomics shows great potential in searching for promising biomarkers. Nonetheless, single omics technology cannot holistically connect the mechanisms with heterogeneity of pathological behavior in CD. The rise of multi-omics analysis integrates genetic/epigenetic profiles with protein/microbial metabolite functionality, providing new hope for comprehensive and in-depth exploration of CD. Herein, we emphasized the different omics features and applications of CD and discussed the current research and limitations of multi-omics in CD. This review will update and deepen our understanding of CD from integration of broad omics spectra and will provide new evidence for targeted individualized therapeutics.
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Affiliation(s)
- Chenlu Mu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qianjing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Qing Zhao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Lijiao Yang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaomeng Li
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Shan-Yu Fung
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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40
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Sinha A, Vaggu RG, Swain R, Patnaik S. Repurposing of RAS-Pathway Mediated Drugs for Intestinal Inflammation Related Diseases for Treating SARS-CoV-2 Infection. Curr Microbiol 2023; 80:194. [PMID: 37106165 PMCID: PMC10136399 DOI: 10.1007/s00284-023-03304-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023]
Abstract
Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is an emerging zoonotic virus, which causes Coronavirus Disease 2019 (COVID-19). Entry of coronaviruses into the cell depends on binding of the viral spike (S) proteins to cellular receptors Angiotensin-converting enzyme 2 (ACE2). The virus-mediated reduction of ACE2/Ang1-7 causes flooding of inflammatory cytokines. A similar scenario of hyper immunologic reaction has been witnessed in the context of Intestinal Inflammatory Diseases (IIDs) with the deregulation of ACE2. This review summarizes several IIDs that lead to such susceptible conditions. It discusses suitable mechanisms of how ACE2, being a crucial regulator of the Renin-Angiotensin System (RAS) signaling pathway, can affect the physiology of intestine as well as lungs, the primary site of SARS-CoV-2 infection. ACE2, as a SARS-CoV-2 receptor, establishes a critical link between COVID-19 and IIDs. Intercessional studies targeting the RAS signaling pathway in patients may provide a novel strategy for addressing the COVID-19 crisis. Hence, the modulation of these key RAS pathway members can be beneficial in both instances. However, it's difficult to say how beneficial are the ACE inhibitors (ACEI)/ Angiotensin II type-1 receptor blockers (ARBs) during COVID-19. As a result, much more research is needed to better understand the relationship between the RAS and SARS-CoV-2 infection.
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Affiliation(s)
- Anupriya Sinha
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, Odisha, 751024, India
| | | | - Ramakrushna Swain
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, Odisha, 751024, India
| | - Srinivas Patnaik
- School of Biotechnology, KIIT University, Campus-XI, Bhubaneswar, Odisha, 751024, India.
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41
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Tian CM, Yang MF, Xu HM, Zhu MZ, Zhang Y, Yao J, Wang LS, Liang YJ, Li DF. Mesenchymal Stem Cell-derived Exosomes: Novel Therapeutic Approach for Inflammatory Bowel Diseases. Stem Cells Int 2023; 2023:4245704. [PMID: 37056457 PMCID: PMC10089786 DOI: 10.1155/2023/4245704] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/19/2023] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
As double membrane-encapsulated nanovesicles (30-150 nm), exosomes (Exos) shuttle between different cells to mediate intercellular communication and transport active cargoes of paracrine factors. The anti-inflammatory and immunomodulatory activities of mesenchymal stem cell (MSC)-derived Exos (MSC-Exos) provide a rationale for novel cell-free therapies for inflammatory bowel disease (IBD). Growing evidence has shown that MSC-Exos can be a potential candidate for treating IBD. In the present review, we summarized the most critical advances in the properties of MSC-Exos, provided the research progress of MSC-Exos in treating IBD, and discussed the molecular mechanisms underlying these effects. Collectively, MSC-Exos had great potential for cell-free therapy in IBD. However, further studies are required to understand the full dimensions of the complex Exo system and how to optimize its effects.
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Affiliation(s)
- Cheng-mei Tian
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
- Department of Emergency, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020 Guangdong, China
| | - Mei-feng Yang
- Department of Hematology, Yantian District People’s Hospital, Shenzhen, Guangdong, China
| | - Hao-ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Min-zheng Zhu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, Guangdong, China
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Li-sheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Yu-jie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning Hospital, Shenzhen, Guangdong, China
| | - De-feng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
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42
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Gowen R, Gamal A, Di Martino L, McCormick TS, Ghannoum MA. Modulating the Microbiome for Crohn's Disease Treatment. Gastroenterology 2023; 164:828-840. [PMID: 36702360 PMCID: PMC10152883 DOI: 10.1053/j.gastro.2023.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/28/2023]
Abstract
The central role of the gut microbiota in the regulation of health and disease has been convincingly demonstrated. Polymicrobial interkingdom interactions between bacterial (the bacteriome) and fungal (the mycobiome) communities of the gut have become a prominent focus for development of potential therapeutic approaches. In addition to polymicrobial interactions, the complex gut ecosystem also mediates interactions between the host and the microbiota. These interactions are complex and bidirectional; microbiota composition can be influenced by host immune response, disease-specific therapeutics, antimicrobial drugs, and overall ecosystems. However, the gut microbiota also influences host immune response to a drug or therapy by potentially transforming the drug's structure and altering bioavailability, activity, or toxicity. This is especially true in cases where the gut microbiota has produced a biofilm. The negative ramifications of biofilm formation include alteration of gut permeability, enhanced antimicrobial resistance, and alteration of host immune response effectiveness. Natural modulation of the gut microbiota, using probiotic and prebiotic approaches, may also be used to affect the host microbiome, a type of "natural" modulation of the host microbiota composition. In this review, we discuss potential bidirectional interactions between microbes and host, and we describe the changes in gut microbiota induced by probiotic and prebiotic approaches as well as their potential clinical consequences, including biofilm formation. We outline a systematic approach to designing probiotics capable of altering the host microbiota in disease states, using Crohn's disease as a model chronic disease. Understanding how the effective changes in the microbiome may enhance treatment efficacy may unlock the possibility of modulating the gut microbiome to improve treatment using a natural approach.
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Affiliation(s)
- Rachael Gowen
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Ahmed Gamal
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Luca Di Martino
- University Hospitals Cleveland Medical Center, Cleveland, Ohio; Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Digestive Health Research Institute, Case Western Reserve University, Cleveland Ohio
| | - Thomas S McCormick
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Mahmoud A Ghannoum
- Department of Dermatology, Case Western Reserve University, Cleveland, Ohio; University Hospitals Cleveland Medical Center, Cleveland, Ohio.
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Bao M, Wang K, Li J, Li Y, Zhu H, Lu M, Zhang Y, Fan Q, Han L, Wang K, Wang D, Gao Y, Peng B, Ming Z, Liu W. ROS Scavenging and inflammation-directed polydopamine nanoparticles regulate gut immunity and flora therapy in inflammatory bowel disease. Acta Biomater 2023; 161:250-264. [PMID: 36863680 DOI: 10.1016/j.actbio.2023.02.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 03/04/2023]
Abstract
Dysfunction of the intestinal mucosal immune system and dysbiosis of the intestinal microflora can induce inflammatory bowel disease. However, drug-mediated clinical treatment remains a challenge due to its poor therapeutic efficacy and severe side effects. Herein, a ROS scavenging and inflammation-directed nanomedicine is designed and fabricated by coupling polydopamine nanoparticles with mCRAMP, an antimicrobial peptide, while wrapping macrophage membrane in the outer layer. The designed nanomedicine reduced the secretion of pro-inflammatory cytokines and elevate the expression of anti-inflammatory cytokine in vivo and in vitro inflammation models, demonstrating its significant ability of improving inflammatory responses. Importantly, the macrophage membrane encapsulated nanoparticles exhibit the obviously enhanced targeting performance in local inflamed tissues. Furthermore, the 16S rRNA sequencing of fecal microorganisms showed that probiotics increased and pathogenic bacteria were inhibited after oral delivery the nanomedicine, indicating that the designed nano platform played a significant role in optimizing intestinal microbiome. Taken together, the designed nanomedicine are not only easy to prepare and exhibit high biocompatibility, but also show the inflammatory targeting property, anti-inflammatory function and positive regulation of intestinal flora, thus providing a new idea for the intervention and treatment of colitis. STATEMENT OF SIGNIFICANCE: Inflammatory bowel disease (IBD), a chronic and intractable disease, may lead to colon cancer in severe cases without effective treatment. However, clinical drugs are largely ineffective owing to insufficient therapeutic efficacies and side effects. Herein, we constructed a biomimetic polydopamine nanoparticle for oral administration to treat the IBD by modulating mucosal immune homeostasis and optimizing intestinal microorganisms. In vitro and in vivo experiments showed that the designed nanomedicine not only exhibits the anti-inflammatory function and inflammatory targeting property but also positively regulate the gut microflora. Taken together, the designed nanomedicine combined immunoregulation and intestinal microecology modulation to significantly enhance the therapeutic effect on colitis in mice, thus providing a new approach for the clinical treatment of colitis.
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Affiliation(s)
- Meiyu Bao
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Keyi Wang
- Department of Urology Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200060, China
| | - Jingqiang Li
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Yueying Li
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200070, China
| | - Huanhuan Zhu
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Meiling Lu
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Yue Zhang
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Qiangyuan Fan
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Lin Han
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Kesheng Wang
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Dongyan Wang
- Department of Gastroenterology, Shanghai Pudong New Area Gongli Hospital, Shanghai 200135, China
| | - Yan Gao
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China
| | - Bo Peng
- Department of Urology Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200060, China.
| | - Zunzhen Ming
- Central Laboratory, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, 301# Yanchang Middle Road, Shanghai, 200072, China.
| | - Weiwei Liu
- Department of Laboratory Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai 200032, China.
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Vuori KA, Hemida M, Moore R, Salin S, Rosendahl S, Anturaniemi J, Hielm-Björkman A. The effect of puppyhood and adolescent diet on the incidence of chronic enteropathy in dogs later in life. Sci Rep 2023; 13:1830. [PMID: 36759678 PMCID: PMC9911636 DOI: 10.1038/s41598-023-27866-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023] Open
Abstract
Diet has a key role in the homeostasis of the gut microenvironment, influencing the microbiome, the gut barrier, host immunity and gut physiology. Yet, there is little information on the role of early diet in the onset of inflammatory gastrointestinal disorders later in life, especially in dogs. Therefore, the aim of the present cross-sectional, epidemiological study with longitudinal data, was to explore associations of companion dogs' early life diet style and food items with owner-reported chronic enteropathy (CE) incidence in later life. Food frequency questionnaire data from Finnish companion dogs was analyzed using principal component analysis and logistic regression. We found that feeding a non-processed meat-based diet and giving the dog human meal leftovers and table scraps during puppyhood (2-6 months) and adolescence (6-18 months) were protective against CE later in life. Especially raw bones and cartilage as well as leftovers and table scraps during puppyhood and adolescence, and berries during puppyhood were associated with less CE. In contrast, feeding an ultra-processed carbohydrate-based diet, namely dry dog food or "kibble" during puppyhood and adolescence, and rawhides during puppyhood were significant risk factors for CE later in life.
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Affiliation(s)
- Kristiina A Vuori
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland.
| | - Manal Hemida
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland.,Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Robin Moore
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Siru Salin
- Department of Agricultural Sciences, Faculty of Agriculture Forestry, University of Helsinki, Helsinki, Finland
| | - Sarah Rosendahl
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Anturaniemi
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Hielm-Björkman
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
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45
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Zhao LP, Wu J, Quan W, Zhou Y, Hong H, Niu GY, Huang SB, Qiao CM, Zhao WJ, Cui C, Shen YQ. DSS-induced acute colitis causes dysregulated tryptophan metabolism in brain: an involvement of gut microbiota. J Nutr Biochem 2023; 115:109282. [PMID: 36758839 DOI: 10.1016/j.jnutbio.2023.109282] [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] [Received: 05/05/2022] [Revised: 01/01/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Inflammatory bowel disease can cause pathological changes of certain organs, including the gut and brain. As the major degradation route of tryptophan (Trp), Kynurenine (Kyn) pathway are involved in multiple pathologies of brain. This study sought to explore the effects of Dextran sulphate sodium (DSS)-induced colitis on serum and brain Trp metabolism (especially the Kyn pathway) and its mechanisms. We induced acute colitis and sub-chronic colitis with 3% DSS and 1% DSS respectively and found more severe intestinal symptoms in acute colitis than sub-chronic colitis. Both of the colitis groups altered Trp-Kyn-Kynurenic acid (Kyna) pathway in serum by regulating the expression of rate-limiting enzyme (IDO-1, KAT2). Interestingly, only 3% DSS group activated Trp-Kyn pathway under the action of metabolic enzymes (IDO-1, TDO-2 and KAT2) in brain. Furthermore, intestinal flora 16S rRNA sequencing showed significantly changes in both DSS-induced colitis groups, including microbial diversity, indicator species, and the abundance of intestinal microflora related to Trp metabolism. The functional pathways of microbiomes involved in inflammation and Trp biosynthesis were elevated after DSS treatment. Moreover, correlation analysis showed a significant association between intestinal flora and Trp metabolism (both in serum and brain). In conclusion, our study suggests that DSS-induced acute colitis causes dysregulation of Trp-Kyn-Kyna pathways of Trp metabolism in serum and brain by affecting rate-limiting enzymes and intestinal flora.
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Affiliation(s)
- Li-Ping Zhao
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Wu
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Quan
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Zhou
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Hong
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Gu-Yu Niu
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Shu-Bing Huang
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Chen-Meng Qiao
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei-Jiang Zhao
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Chun Cui
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan-Qin Shen
- Neurodegeneration and Injury Laboratory, Wuxi Medical School, Jiangnan University, Wuxi, Jiangsu, China.
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46
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Bay M C, Núñez F P, Quera R, Yarur AJ. Current perspectives on pediatric inflammatory bowel disease focusing on transitional care management. What should we consider? GASTROENTEROLOGIA Y HEPATOLOGIA 2023; 46:139-147. [PMID: 36243253 DOI: 10.1016/j.gastrohep.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 11/25/2022]
Abstract
The prevalence of inflammatory bowel disease (IBD) continues to rise around the globe. Although the percentage of pediatric IBD patients seems to be increasing, rates are surprisingly heterogeneous among different populations. Although the pathogenesis of IBD is believed to be multifactorial, a genetic predisposition may be especially relevant in pediatric-onset IBD. Phenotypic characteristics can also be significantly different when comparing pediatric and adult-onset IBD. Patients that develop the disease at a younger age usually present with more extensive and more aggressive disease and develop complications faster when compared to those that develop it during adulthood. Children with IBD are found to have frequent mood disorders and have a higher risk of developing socio-economic hardship, failing to meet development milestones. Therefore, IBD management should always involve a multidisciplinary team that is not limited to medical providers. Most institutions do not have an established transition protocol and lack the resources and training for transition care. Although there is no consensus on an optimal timing to transition the patient's care to an adult team, it is usually accepted they should be eligible for adult care when most of the key transition points have been met. Management strategies should be tailored to each patient's developmental level and environment. A successful transition can improve the long-term outcomes such as sustained remission, medication adherence, mental health and social and academic performance, while decreasing healthcare utilization. Every institution that manages pediatric IBD patients should have a well-established transition protocol in order to make sure to maintain continuity of care.
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Affiliation(s)
- Constanza Bay M
- Department of Pediatrics, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Paulina Núñez F
- Department of Gastroenterology, Hospital San Juan De Dios, Universidad de Chile, Inflammatory Bowel Disease Programm, Digestive Disease Center, Clínica Universidad de los Andes, Universidad de los Andes, Santiago 7620157, Chile.
| | - Rodrigo Quera
- Inflammatory Bowel Disease Programm, Digestive Disease Center, Clínica Universidad de los Andes, Universidad de los Andes, Santiago 7620157, Chile
| | - Andrés J Yarur
- Cedars-Sinai Medical Center, 8730 Alden Dr. Thalians 2E, Los Angeles, CA 90048, USA
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47
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Saadh MJ, Mikhailova MV, Rasoolzadegan S, Falaki M, Akhavanfar R, Gonzáles JLA, Rigi A, Kiasari BA. Therapeutic potential of mesenchymal stem/stromal cells (MSCs)-based cell therapy for inflammatory bowel diseases (IBD) therapy. Eur J Med Res 2023; 28:47. [PMID: 36707899 PMCID: PMC9881387 DOI: 10.1186/s40001-023-01008-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/10/2023] [Indexed: 01/28/2023] Open
Abstract
Recently, mesenchymal stem/stromal cells (MSCs) therapy has become an emerging therapeutic modality for the treatment of inflammatory bowel disease (IBD), given their immunoregulatory and pro-survival attributes. MSCs alleviate dysregulated inflammatory responses through the secretion of a myriad of anti-inflammatory mediators, such as interleukin 10 (IL-10), transforming growth factor-β (TGFβ), prostaglandin E2 (PGE2), tumor necrosis factor-stimulated gene-6 (TSG-6), etc. Indeed, MSC treatment of IBD is largely carried out through local microcirculation construction, colonization and repair, and immunomodulation, thus alleviating diseases severity. The clinical therapeutic efficacy relies on to the marked secretion of various secretory molecules from viable MSCs via paracrine mechanisms that are required for gut immuno-microbiota regulation and the proliferation and differentiation of surrounding cells like intestinal epithelial cells (IECs) and intestinal stem cells (ISCs). For example, MSCs can induce IECs proliferation and upregulate the expression of tight junction (TJs)-associated protein, ensuring intestinal barrier integrity. Concerning the encouraging results derived from animal studies, various clinical trials are conducted or ongoing to address the safety and efficacy of MSCs administration in IBD patients. Although the safety and short-term efficacy of MSCs administration have been evinced, the long-term efficacy of MSCs transplantation has not yet been verified. Herein, we have emphasized the illumination of the therapeutic capacity of MSCs therapy, including naïve MSCs, preconditioned MSCs, and also MSCs-derived exosomes, to alleviate IBD severity in experimental models. Also, a brief overview of published clinical trials in IBD patients has been delivered.
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Affiliation(s)
- Mohamed J. Saadh
- Department of Basic Sciences, Faculty of Pharmacy, Middle East University, Amman, 11831 Jordan
| | - Maria V. Mikhailova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Soheil Rasoolzadegan
- Department of Surgery, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojgan Falaki
- Department of Internal Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roozbeh Akhavanfar
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Amir Rigi
- Department of Nursing, Young Researchers and Elite Club, Zahedan Branch, Azad University, Zahedan, Iran
| | - Bahman Abedi Kiasari
- Virology Department, Faculty of Veterinary Medicine, The University of Tehran, Tehran, Iran
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48
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Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models. Sci Rep 2023; 13:203. [PMID: 36604447 PMCID: PMC9814625 DOI: 10.1038/s41598-022-26816-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. A clear gap in our existing CD diagnostics and current disease management approaches is the lack of highly specific biomarkers that can be used to streamline or personalize disease management. Comprehensive profiling of metabolites holds promise; however, these high-dimensional profiles need to be reduced to have relevance in the context of CD. Machine learning approaches are optimally suited to bridge this gap in knowledge by contextualizing the metabolic alterations in CD using genome-scale metabolic network reconstructions. Our work presents a framework for studying altered metabolic reactions between patients with CD and controls using publicly available transcriptomic data and existing gene-driven metabolic network reconstructions. Additionally, we apply the same methods to patient-derived ileal enteroids to explore the utility of using this experimental in vitro platform for studying CD. Furthermore, we have piloted an untargeted metabolomics approach as a proof-of-concept validation strategy in human ileal mucosal tissue. These findings suggest that in silico metabolic modeling can potentially identify pathways of clinical relevance in CD, paving the way for the future discovery of novel diagnostic biomarkers and therapeutic targets.
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49
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Panah FM, Nielsen KD, Simpson GL, Schönherz A, Schramm A, Lauridsen C, Nielsen TS, Højberg O, Fredborg M, Purup S, Canibe N. A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis. Front Microbiol 2023; 14:1018242. [PMID: 37138607 PMCID: PMC10150118 DOI: 10.3389/fmicb.2023.1018242] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Ulcerative colitis (UC) is characterized by chronic inflammation in the colonic epithelium and has a blurred etiology. A western diet and microbial dysbiosis in the colon were reported to play a role in UC development. In this study, we investigated the effect of a westernized diet, i.e., increasing fat and protein content by including ground beef, on the colonic bacterial composition in a dextran sulfate sodium (DexSS) challenged pig study. Methods The experiment was carried out in three complete blocks following a 2×2 factorial design including 24 six-week old pigs, fed either a standard diet (CT) or the standard diet substituted with 15% ground beef to simulate a typical westernized diet (WD). Colitis was induced in half of the pigs on each dietary treatment by oral administration of DexSS (DSS and WD+DSS, respectively). Samples from proximal and distal colon and feces were collected. Results and discussion Bacterial alpha diversity was unaffected by experimental block, and sample type. In proximal colon, WD group had similar alpha diversity to CT group and the WD+DSS group showed the lowest alpha diversity compared to the other treatment groups. There was a significant interaction between western diet and DexSS for beta diversity, based on Bray-Curtis dissimilarly. The westernized diet and DexSS resulted in three and seven differentially abundant phyla, 21 and 65 species, respectively, mainly associated with the Firmicutes and Bacteroidota phyla followed by Spirochaetota, Desulfobacterota, and Proteobacteria. The concentration of short-chain fatty acids (SCFA) was lowest in the distal colon. Treatment had a slight effect on the estimates for microbial metabolites that might have valuable biological relevance for future studies. The concentration of putrescine in the colon and feces and that of total biogenic amines was highest in the WD+DSS group. We conclude that a westernized diet could be a potential risk factor and an exacerbating agent for UC by reducing the abundance of SCFA-producing bacteria, increasing the abundance of pathogens such as Helicobacter trogontum, and by increasing the concentration of microbial proteolytic-derived metabolites in the colon.
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Affiliation(s)
- Farhad M. Panah
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
- *Correspondence: Farhad M. Panah,
| | - Katrine D. Nielsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Gavin L. Simpson
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Anna Schönherz
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | | | - Charlotte Lauridsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Tina S. Nielsen
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Ole Højberg
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Marlene Fredborg
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Stig Purup
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
| | - Nuria Canibe
- Department of Veterinary and Animal Sciences, Aarhus University, Tjele, Denmark
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50
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Kanyongo W, Ezugwu AE. Machine learning approaches to medication adherence amongst NCD patients: A systematic literature review. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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