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Chew DCH, Khoo XH, Lee TS, Chin KY, Raja Ali RA, Muhammad Nawawi KN, Wan Ibrahim NR, Hilmi I. A Systematic Review on the Increasing Incidence of Inflammatory Bowel Disease in Southeast Asia: Looking Beyond the Urbanization Phenomenon. Inflamm Bowel Dis 2024; 30:1566-1578. [PMID: 37935628 DOI: 10.1093/ibd/izad189] [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: 02/15/2023] [Indexed: 11/09/2023]
Abstract
The incidence of inflammatory bowel disease (IBD) has been increasing in Southeast Asia (SEA) in tandem with its economic growth and urbanization over the past 2 decades. Specific characteristics of IBD in SEA are similar to East Asia and the West, such as the declining ratio of ulcerative colitis to Crohn's disease. However, exceptionally low familial aggregation is seen. Smoking is also not a common risk factor in patients with Crohn's disease. The incidence of perianal disease is higher in SEA than in Australia and is comparable to the West. In a multiracial population, such as Singapore and Malaysia, Indians have the highest incidence and prevalence rates, which are likely to be due to important putative mutations. For instance, a higher frequency of the NOD2 predisposing mutation SNP5 and IBD risk allele IGR2198a and IGR2092a were found in Indians. Although differences in the genetic constitution play an important role in the epidemiology and prognosis of IBD in SEA, the emergence of this disease offers a unique opportunity to identify potential exposomes that contribute to its pathogenesis.
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Affiliation(s)
- Deborah Chia Hsin Chew
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Xin-Hui Khoo
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tiong See Lee
- Department of Gastroenterology and Hepatology, Selayang Hospital, Kuala Lumpur, Malaysia
| | - Kok-Yong Chin
- Department of Pharmacology, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Khairul Najmi Muhammad Nawawi
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Graça M, Nobre R, Sousa L, Ilic A. Distributed transformer for high order epistasis detection in large-scale datasets. Sci Rep 2024; 14:14579. [PMID: 38918413 PMCID: PMC11199512 DOI: 10.1038/s41598-024-65317-5] [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: 02/24/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Understanding the genetic basis of complex diseases is one of the most important challenges in current precision medicine. To this end, Genome-Wide Association Studies aim to correlate Single Nucleotide Polymorphisms (SNPs) to the presence or absence of certain traits. However, these studies do not consider interactions between several SNPs, known as epistasis, which explain most genetic diseases. Analyzing SNP combinations to detect epistasis is a major computational task, due to the enormous search space. A possible solution is to employ deep learning strategies for genomic prediction, but the lack of explainability derived from the black-box nature of neural networks is a challenge yet to be addressed. Herein, a novel, flexible, portable, and scalable framework for network interpretation based on transformers is proposed to tackle any-order epistasis. The results on various epistasis scenarios show that the proposed framework outperforms state-of-the-art methods for explainability, while being scalable to large datasets and portable to various deep learning accelerators. The proposed framework is validated on three WTCCC datasets, identifying SNPs related to genes known in the literature that have direct relationships with the studied diseases.
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Affiliation(s)
- Miguel Graça
- INESC-ID, Instituto Superior Técnico, 1000-029, Lisbon, Portugal.
| | - Ricardo Nobre
- INESC-ID, Instituto Superior Técnico, 1000-029, Lisbon, Portugal
| | - Leonel Sousa
- INESC-ID, Instituto Superior Técnico, 1000-029, Lisbon, Portugal
| | - Aleksandar Ilic
- INESC-ID, Instituto Superior Técnico, 1000-029, Lisbon, Portugal
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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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Song XQ, Li Q, Zhang J. A double-edged sword: DLG5 in diseases. Biomed Pharmacother 2023; 162:114611. [PMID: 37001186 DOI: 10.1016/j.biopha.2023.114611] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
Discs large homolog 5 (DLG5), a key member of the membrane-associated guanylate kinase (MAGUKs) family, is a scaffold molecule for signal transduction complexes and is responsible for assembling receptors and adapters. This scaffold protein stabilizes adhesion and tight bonding complexes in many organs and tissues, and is involved of maintaining epithelial polarity. Although DLG5 plays a role in normal development in mice, it has also been linked to the onset and development of several diseases, particularly Crohn's disease and various malignancies. DLG5 has been shown to impact the progression of cancer through direct or indirect interactions with H-catenin, E-cadherin, Vimentin, p53, P21, Cyclin D1, TGF-β1, AKT, Hippo, and classic G protein signaling pathways. DLG5 and DLG5 variants has been found to have a dual role in human diseases. Although it is overexpressed in pancreatic adenocarcinoma, its expression is reduced in lung, liver, breast, prostate, and bladder cancers. However, two independent studies on glioblastoma (GBM) have shown the opposite effects of DLG5. Our study evaluates the existing literature on the role of DLG5 and DLG5 variants in disease processes, and summarizes the available data on the role of DLG5 in disease based on cell experiments, clinical samples, and animal models, while highlighting its future potential in disease treatment.
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Castillo-Azofeifa D, Wald T, Reyes EA, Gallagher A, Schanin J, Vlachos S, Lamarche-Vane N, Bomidi C, Blutt S, Estes MK, Nystul T, Klein OD. A DLG1-ARHGAP31-CDC42 axis is essential for the intestinal stem cell response to fluctuating niche Wnt signaling. Cell Stem Cell 2023; 30:188-206.e6. [PMID: 36640764 PMCID: PMC9922544 DOI: 10.1016/j.stem.2022.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/13/2022] [Accepted: 12/12/2022] [Indexed: 01/15/2023]
Abstract
A central factor in the maintenance of tissue integrity is the response of stem cells to variations in the levels of niche signals. In the gut, intestinal stem cells (ISCs) depend on Wnt ligands for self-renewal and proliferation. Transient increases in Wnt signaling promote regeneration after injury or in inflammatory bowel diseases, whereas constitutive activation of this pathway leads to colorectal cancer. Here, we report that Discs large 1 (Dlg1), although dispensable for polarity and cellular turnover during intestinal homeostasis, is required for ISC survival in the context of increased Wnt signaling. RNA sequencing (RNA-seq) and genetic mouse models demonstrated that DLG1 regulates the cellular response to increased canonical Wnt ligands. This occurs via the transcriptional regulation of Arhgap31, a GTPase-activating protein that deactivates CDC42, an effector of the non-canonical Wnt pathway. These findings reveal a DLG1-ARHGAP31-CDC42 axis that is essential for the ISC response to increased niche Wnt signaling.
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Affiliation(s)
- David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Regenerative Medicine, Genentech, Inc., South San Francisco, CA, USA
| | - Tomas Wald
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Efren A Reyes
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pharmaceutical Chemistry and TETRAD Program, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron Gallagher
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Julia Schanin
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Stephanie Vlachos
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Nathalie Lamarche-Vane
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Carolyn Bomidi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Todd Nystul
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Johnson TO, Akinsanmi AO, Ejembi SA, Adeyemi OE, Oche JR, Johnson GI, Adegboyega AE. Modern drug discovery for inflammatory bowel disease: The role of computational methods. World J Gastroenterol 2023; 29:310-331. [PMID: 36687123 PMCID: PMC9846937 DOI: 10.3748/wjg.v29.i2.310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) comprising ulcerative colitis, Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract. IBD has spread around the world and is becoming more prevalent at an alarming rate in developing countries whose societies have become more westernized. Cell therapy, intestinal microecology, apheresis therapy, exosome therapy and small molecules are emerging therapeutic options for IBD. Currently, it is thought that low-molecular-mass substances with good oral bio-availability and the ability to permeate the cell membrane to regulate the action of elements of the inflammatory signaling pathway are effective therapeutic options for the treatment of IBD. Several small molecule inhibitors are being developed as a promising alternative for IBD therapy. The use of highly efficient and time-saving techniques, such as computational methods, is still a viable option for the development of these small molecule drugs. The computer-aided (in silico) discovery approach is one drug development technique that has mostly proven efficacy. Computational approaches when combined with traditional drug development methodology dramatically boost the likelihood of drug discovery in a sustainable and cost-effective manner. This review focuses on the modern drug discovery approaches for the design of novel IBD drugs with an emphasis on the role of computational methods. Some computational approaches to IBD genomic studies, target identification, and virtual screening for the discovery of new drugs and in the repurposing of existing drugs are discussed.
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Affiliation(s)
| | | | | | | | - Jane-Rose Oche
- Department of Biochemistry, University of Jos, Jos 930222, Plateau, Nigeria
| | - Grace Inioluwa Johnson
- Faculty of Clinical Sciences, College of Health Sciences, University of Jos, Jos 930222, Plateau, Nigeria
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López-Cauce B, Puerto M, García JJ, Ponce-Alonso M, Becerra-Aparicio F, del Campo R, Peligros I, Fernández-Aceñero MJ, Gómez-Navarro Y, Lara JM, Miranda-Bautista J, Marín-Jiménez I, Bañares R, Menchén L. Akkermansia deficiency and mucin depletion are implicated in intestinal barrier dysfunction as earlier event in the development of inflammation in interleukin-10-deficient mice. Front Microbiol 2023; 13:1083884. [PMID: 36699599 PMCID: PMC9869054 DOI: 10.3389/fmicb.2022.1083884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Background Dysbiosis and mucin depletion are related with intestinal barrier dysfunction and seems to be an early pathophysiological event in inflammatory bowel disease (IBD). The objective of this work is to study these parameters in the natural history of colitis in IL-10 deficient mice (IL-10-/-). Methods Wild type (WT) and IL-10-/-. mice were followed until sacrifice at 3, 5, 10, 20, 57, and 70 weeks. Body weight, colonic weight/length ratio and in vivo intestinal permeability were registered. Expression of inflammatory and adhesion molecules in the colon was explored by qPCR as Mucin-2 (MUC-2) and molecules involved in goblet cell maturation Interleukin-18 (IL-18) and WAP Four-Disulfide Core Domain 2 (WFDC2), the endoplasmic reticulum stress markers X-box-binding protein (Xbp-1) and Reticulon-4B (RTN-4B). Bacterial composition in feces and colonic mucosa was determined by massive sequencing of the V3-V4 regions of 16S rDNA gene. Results IL-10-/- mice showed histological inflammation at weeks 20 and 57, but most notably the intestinal permeability was significantly higher from week 10. Concordantly, the number of goblet cells and expression of MUC-2, IL-18, WFDC2 and Xbp-1 were significantly lower in KO from week 10. Nevertheless, no significant differences were found in the mRNA expression of MUC-2 or Xbp-1 between both groups-derived colon organoids. Significant bacterial differences began at week 5, being the Akkermansia deficiency in KO the most relevant result. Conclusion Gut microbiota alterations and mucin depletion are associated with early intestinal barrier dysfunction and precede overt gut inflammation in this animal model of IBD.
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Affiliation(s)
- Beatriz López-Cauce
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Microbiología y Parasitología Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Marta Puerto
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Juan José García
- Departamento de Microbiología y Parasitología Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Ramón y Cajal, CIBERINFEC, IRYCIS, Madrid, Spain
| | | | - Rosa del Campo
- Servicio de Microbiología, Hospital Ramón y Cajal, CIBERINFEC, IRYCIS, Madrid, Spain
| | - Isabel Peligros
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - Yésica Gómez-Navarro
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - José M. Lara
- Servicio de Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - José Miranda-Bautista
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ignacio Marín-Jiménez
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Rafael Bañares
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Medicina, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Luis Menchén
- Servicio de Aparato Digestivo, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain,Departamento de Medicina, Facultad de Medicina, Universidad Complutense, Madrid, Spain,*Correspondence: Luis Menchén,
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Yin R, Neyens DM. Online Health Resource Use by Individuals With Inflammatory Bowel Disease: Analysis Using the National Health Interview Survey. J Med Internet Res 2020; 22:e15352. [PMID: 32969831 PMCID: PMC7545328 DOI: 10.2196/15352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 01/28/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Background The internet has enabled convenient and efficient health information searching which is valuable for individuals with chronic conditions requiring some level of self-management. However, there is little research evaluating what factors may impact the use of the internet for health-related tasks for specific clinical populations, such as individuals with inflammatory bowel diseases. Objective Our goal was to investigate the factors that influence internet use in acquiring health information by individuals with inflammatory bowel diseases. Specifically, we identified factors associated with internet searching behavior and using the internet for completing health-related tasks. Methods We used 2016 National Health Interview Survey weighted data to develop logistic regression models to predict the likelihood that individuals with inflammatory bowel diseases would use the internet for 2 types of tasks: seeking health information through online searches and using the internet to perform health-related tasks including scheduling appointments and emailing care providers. Results 2016 National Health Interview Survey weighted data include more than 3 million weighted adult respondents with inflammatory bowel diseases (approximately 1.29% of adults in the weighted data set). Our results suggest that approximately 66.3% of those with inflammatory bowel diseases reported using the internet at least once a day, and approximately 14.7% reported being dissatisfied with their current health care. About 62.3% of those with inflammatory bowel diseases reported that they had looked up health information online, 16.3% of those with inflammatory bowel diseases reported that they had scheduled an appointment with a health care provider online, and 21.6% reported having used a computer to communicate with a health provider by email. We found that women who were self-regulating their care were more likely to look up health information online than others. Both middle-aged and older adults with inflammatory bowel diseases who were unsatisfied with their current health care were less likely to look up health information online. Frequent internet users who were worried about medical costs were more likely to look up health information online. Similarly, the results from our statistical models suggest that individuals with inflammatory bowel diseases who were frequent internet users were more likely to use the internet for specific health-related tasks. Additionally, women with inflammatory bowel diseases who reported being married were less likely to use the internet for specific health-related tasks. Conclusions For those with inflammatory bowel diseases, there are additional socioeconomic and behavioral factors that impact the use of the internet for health information and health-related tasks. Future research should evaluate how these factors moderate the use of the internet and identify how online resources can support clinical populations in ways that improve access to information, support health self-management, and subsequently improve health outcomes.
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Affiliation(s)
- Rong Yin
- Department of Industrial Engineering, Clemson University, Clemson, SC, United States
| | - David M Neyens
- Department of Industrial Engineering, Clemson University, Clemson, SC, United States
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10
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Giudici F, Lombardelli L, Russo E, Cavalli T, Zambonin D, Logiodice F, Kullolli O, Giusti L, Bargellini T, Fazi M, Biancone L, Scaringi S, Clemente AM, Perissi E, Delfino G, Torcia MG, Ficari F, Tonelli F, Piccinni MP, Malentacchi C. Multiplex gene expression profile in inflamed mucosa of patients with Crohn’s disease ileal localization: A pilot study. World J Clin Cases 2019; 7:2463-2476. [PMID: 31559282 PMCID: PMC6745337 DOI: 10.12998/wjcc.v7.i17.2463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Crohn’s disease (CD) is a complex disorder resulting from the interaction of genetic, environmental, and microbial factors. The pathogenic process may potentially affect any segment of the gastrointestinal tract, but a selective location in the terminal ileum was reported in 50% of patients.
AIM To characterize clinical sub-phenotypes (colonic and/or ileal) within the same disease, in order to identify new therapeutic targets.
METHODS 14 consecutive patients undergoing surgery for ileal CD were recruited for this study. Peripheral blood samples from each patient were collected and the main polymorphisms of the gene Card15/Nod2 (R702W, G908R, and 1007fs) were analyzed in each sample. In addition, tissue samples were taken from both the tract affected by CD and from the apparently healthy and disease-free margins (internal controls). We used a multiplex gene assay in specimens obtained from patients with ileal localization of CD to evaluate the simultaneous expression of 24 genes involved in the pathogenesis of the disease. We also processed surgery gut samples with routine light microscopy (LM) and transmission electron microscopy (TEM) techniques to evaluate their structural and ultrastructural features.
RESULTS We found a significant increase of Th17 (IL17A and IL17F, IL 23R and CCR6) and Th1 (IFN-γ) gene expression in inflamed mucosa compared to non-inflamed sites of 14 CD patients. DEFB4 and HAMP, two genes coding for antimicrobial peptides, were also strongly activated in inflamed ileal mucosa, suggesting the overwhelming stimulation of epithelial cells by commensal microbiota. IFN-γ and CCR6 were more expressed in inflamed mucosa of CD patients with ileal localization compared with patients with colonic localization suggesting a more aggressive inflammation process in this site. Morphological analysis of the epithelial lining of Lieberkün crypts disclosed enhanced release activity from goblet mucocytes, whereas the lamina propria contained numerous cells pertaining to various lines.
CONCLUSION We observed that the expression of ileal genes related to Th1 and Th17 activity is strongly activated as well as the expression of genes involved in microbiota regulation.
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Affiliation(s)
- Francesco Giudici
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Letizia Lombardelli
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Edda Russo
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Tiziana Cavalli
- Dipartimento Chirurgico Ortopedico, Ospedale Carlo Poma di Mantova, Firenze 50134, Italy
| | - Daniela Zambonin
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Federica Logiodice
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Ornela Kullolli
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Lamberto Giusti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
| | - Tatiana Bargellini
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Marilena Fazi
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Livia Biancone
- Department of Internal Medicine, University of Roma Tor Vergata, Roma 00133, Italy
| | - Stefano Scaringi
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Ann Maria Clemente
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Eloisa Perissi
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Giovanni Delfino
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
| | - Maria G Torcia
- Marie- Pierre Piccinni, Department of Experimental and Clinical Medicine, University of Firenze, Firenze 50134, Italy
| | - Ferdinando Ficari
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | - Francesco Tonelli
- Surgical Unit, Department of Surgery and Translational Medicine, University of Firenze, Firenze 50134, Italy
| | | | - Cecilia Malentacchi
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Firenze, Firenze 50134, Italy
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Gao Z, Sun L, Dai K, Du Y, Wu S, Bao W. Effects of mutations in porcine miRNA-215 precursor sequences on miRNA-215 regulatory function. Gene 2019; 701:131-138. [PMID: 30905811 DOI: 10.1016/j.gene.2019.03.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/12/2019] [Accepted: 03/20/2019] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) play an important role in animal growth and disease development, and sequence variation in microRNAs can alter their functions. Herein, we explored the effects of mutations in the miRNA-215 precursor sequence on the miRNA-215 regulatory network and resistance to Escherichia coli (E. coli). Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) was used to detect sequence variations in Sutai and Meishan pigs. The miR-192 precursor sequence was not mutated, but the miR-215 precursor included an AT insertion mutation at position 6 (start from the first base of the miR-215 precursor) and a C/T mutation at position 43. Wild-type (WT) and mutant miR-215 precursor expression vectors were constructed to investigate the effects of sequence variation on expression of miR-215 and its target genes DLG5 and ALCAM, cytokine levels and E. coli adhesion. Compared with the WT control group, cells harbouring the C/T mutant vector displayed reduced miR-215 expression, increased target gene expression, elevated cytokine levels and rising E. coli adhesion, whereas cells harbouring the AT insertion mutant vector were not significantly changed. The sequence variation in the miRNA-215 precursor may affect the miRNA-215 regulatory network, and alter the stability of intestinal epithelial cells (IPEC-J2 cells) and resistance to E. coli. Our findings provide guidance for future research on the regulatory mechanisms of miR-215 in porcine resistance to E. coli F18, and identifying effective genetic markers against this organism.
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Affiliation(s)
- Zhongcheng Gao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Kaiyu Dai
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yulu Du
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Jiangsu, Yangzhou, 225009, China.
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12
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Cellular and Molecular Therapeutic Targets in Inflammatory Bowel Disease-Focusing on Intestinal Barrier Function. Cells 2019; 8:cells8020193. [PMID: 30813280 PMCID: PMC6407030 DOI: 10.3390/cells8020193] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 02/18/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023] Open
Abstract
The human gut relies on several cellular and molecular mechanisms to allow for an intact and dynamical intestinal barrier. Normally, only small amounts of luminal content pass the mucosa, however, if the control is broken it can lead to enhanced passage, which might damage the mucosa, leading to pathological conditions, such as inflammatory bowel disease (IBD). It is well established that genetic, environmental, and immunological factors all contribute in the pathogenesis of IBD, and a disturbed intestinal barrier function has become a hallmark of the disease. Genetical studies support the involvement of intestinal barrier as several susceptibility genes for IBD encode proteins with key functions in gut barrier and homeostasis. IBD patients are associated with loss in bacterial diversity and shifts in the microbiota, with a possible link to local inflammation. Furthermore, alterations of immune cells and several neuro-immune signaling pathways in the lamina propria have been demonstrated. An inappropriate immune activation might lead to mucosal inflammation, with elevated secretion of pro-inflammatory cytokines that can affect the epithelium and promote a leakier barrier. This review will focus on the main cells and molecular mechanisms in IBD and how these can be targeted in order to improve intestinal barrier function and reduce inflammation.
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13
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Single Nucleotide Polymorphisms in Selected Genes in Inflammatory Bowel Disease. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6914346. [PMID: 30648106 PMCID: PMC6311883 DOI: 10.1155/2018/6914346] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 12/04/2018] [Indexed: 12/29/2022]
Abstract
Introduction Inflammatory bowel disease (IBD) is a complicated, multifunctional disorder characterized by chronic, recurring inflammation of the digestive tract. The two main types of IBD are ulcerative colitis (UC) and Crohn's disease (CD). The aim of the study was to determine single nucleotide polymorphism in fragments of the genes CARD15/NOD2 and DLG5 in patients from the Lublin Voivodeship. Patients and Methods The study was carried out in Lublin (Poland) in 2016. 27 individuals participated in the research. The research group comprised 9 patients with a diagnosis of Crohn's disease and 9 with ulcerative colitis, aged 20 to 48, and 9 healthy volunteers. Results No SNPs were confirmed for the CARD15/NOD2 gene fragment, but a substitution (T>C) was found in the DLG5 gene in a Crohn's disease patient. Conclusion Absence of extraintestinal symptoms in patients with Crohn's disease may be associated with the absence of CARD15/NOD2 SNPs. The study suggests that SNPs (T>C substitution) affect the function of the DLG5 protein and thus play a role in the development of IBD, in particular Crohn's disease. The analysis presented is a pilot study due to the small number of samples.
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14
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Zhang Z, Zhang Q, Xiao Q, Sun H, Gao H, Yang Y, Chen J, Li Z, Xue M, Ma P, Yang H, Xu N, Wang Q, Pan Y. Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data. Anim Genet 2018; 49:579-591. [DOI: 10.1111/age.12730] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Zhe Zhang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Qianqian Zhang
- Animal Genetics, Bioinformatics and Breeding; University of Copenhagen; Frederiksberg 1870 Denmark
| | - Qian Xiao
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hao Sun
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; 8830 Tjele Denmark
| | - Yumei Yang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Jiucheng Chen
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Zhengcao Li
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Ming Xue
- National Station of Animal Husbandry; Beijing 100125 China
| | - Peipei Ma
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongjie Yang
- National Station of Animal Husbandry; Beijing 100125 China
| | - Ningying Xu
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Qishan Wang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Yuchun Pan
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
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15
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Katsanos KH, Papadakis KA. Inflammatory Bowel Disease: Updates on Molecular Targets for Biologics. Gut Liver 2018; 11:455-463. [PMID: 28486793 PMCID: PMC5491079 DOI: 10.5009/gnl16308] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/03/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022] Open
Abstract
Therapy for inflammatory bowel disease (IBD) has changed, with several new agents being evaluated. The era of anti-tumor necrosis factor (anti-TNF) antibody therapy saw remarkable progress in IBD therapy. Some patients, however, do not respond to anti-TNF treatment, or their response decreases over time. This phenomenon highlights the need to identify new molecular targets for therapy in IBD. The targets of new therapeutic molecules in IBD must aim to restore immune dysregulation by the inhibition of proinflammatory cytokines (TNF-α, interleukin [IL]-6, IL-13, IL-17, IL-18, and IL-21) and augmentation of the effect of anti-inflammatory cytokines (IL-10, IL-11, and transforming growth factor β) and to pursue new anti-inflammatory targets, such as regulatory T-cell therapy, Smad7 antisense, Janus-activated kinase inhibition, Toll-like receptor stimulation, leukocyte adhesion, and blockade of T-cell homing via integrins and mucosal addressin cellular adhesion molecule-1. In addition, potential molecular targets could restore mucosal barrier function and stimulate mucosal healing. Despite these potential targets, the value and clinical significance of most new molecules remain unclear, and clinical efficacy and safety must be better defined before their implementation in clinical practice. This article aims to review the promising and emerging molecular targets that could be clinically meaningful for novel therapeutic approaches.
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Affiliation(s)
- Konstantinos H Katsanos
- Division of Gastroenterology, Department of Internal Medicine, University of Ioannina School of Health Sciences, Ioannina, Greece
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16
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Saito Y, Desai RR, Muthuswamy SK. Reinterpreting polarity and cancer: The changing landscape from tumor suppression to tumor promotion. Biochim Biophys Acta Rev Cancer 2018; 1869:103-116. [DOI: 10.1016/j.bbcan.2017.12.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 12/21/2022]
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17
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Insight into the molecular mechanism of miR-192 regulating Escherichia coli resistance in piglets. Biosci Rep 2018; 38:BSR20171160. [PMID: 29363554 PMCID: PMC5821941 DOI: 10.1042/bsr20171160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 12/31/2017] [Accepted: 01/23/2018] [Indexed: 11/21/2022] Open
Abstract
MicroRNAs (miRNAs) have important roles in many cellular processes, including cell proliferation, growth and development, and disease control. Previous study demonstrated that the expression of two highly homologous miRNAs (miR-192 and miR-215) was up-regulated in weaned piglets with Escherichia coli F18 infection. However, the potential molecular mechanism of miR-192 in regulating E. coli infection remains unclear in pigs. In the present study, we analyzed the relationship between level of miR-192 and degree of E. coli resistance using transcription activator-like effector nuclease (TALEN), in vitro bacterial adhesion assays, and target genes research. A TALEN expression vector that specifically recognizes the pig miR-192 was constructed and then monoclonal epithelial cells defective in miR-192 were established. We found that miR-192 knockout led to enhance the adhesion ability of the E. coli strains F18ab, F18ac and K88ac, meanwhile increase the expression of target genes (DLG5 and ALCAM) by qPCR and Western blotting analysis. The results suggested that miR-192 and its key target genes (DLG5 and ALCAM) could have a key role in E. coli infection. Based on our findings, we propose that further investigation of miR-192 function is likely to lead to insights into the molecular mechanisms of E. coli infection.
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18
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Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt MT, Krawczak M, Schreiber S, Rosenstiel P. Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease. Gut 2017; 66:2087-2097. [PMID: 27694142 PMCID: PMC5749366 DOI: 10.1136/gutjnl-2016-311651] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/15/2016] [Accepted: 08/14/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVE An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD. DESIGN Mucosal biopsies from Crohn's disease and patients with UC, disease controls and healthy individuals (n=63) were subjected to microbiome, transcriptome and splicing analysis, employing next-generation sequencing. The three data levels were integrated by different bioinformatic approaches, including systems biology-inspired network and pathway analysis. RESULTS Microbiota, host transcript levels and host splicing patterns were influenced most strongly by tissue differences, followed by the effect of inflammation. Both factors point towards a substantial disease-related alteration of metabolic processes. We also observed a strong enrichment of splicing events in inflamed tissues, accompanied by an alteration of the mucosa-attached bacterial taxa. Finally, we noted a striking uncoupling of the three molecular entities when moving from healthy individuals via disease controls to patients with IBD. CONCLUSIONS Our results provide strong evidence that the interplay between microbiome and host transcriptome, which normally characterises a state of intestinal homeostasis, is drastically perturbed in Crohn's disease and UC. Consequently, integrating multiple OMICs levels appears to be a promising approach to further disentangle the complexity of IBD.
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Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Carolin Knecht
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Berenice Brandt
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Sascha Schäuble
- Language and Information Engineering Lab, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Fretter
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany,Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
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19
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Campanale JP, Sun TY, Montell DJ. Development and dynamics of cell polarity at a glance. J Cell Sci 2017; 130:1201-1207. [PMID: 28365593 DOI: 10.1242/jcs.188599] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cells exhibit morphological and molecular asymmetries that are broadly categorized as cell polarity. The cell polarity established in early embryos prefigures the macroscopic anatomical asymmetries characteristic of adult animals. For example, eggs and early embryos have polarized distributions of RNAs and proteins that generate global anterior/posterior and dorsal/ventral axes. The molecular programs that polarize embryos are subsequently reused in multiple contexts. Epithelial cells require apical/basal polarity to establish their barrier function. Migrating cells polarize in the direction of movement, creating distinct leading and trailing structures. Asymmetrically dividing stem cells partition different molecules between themselves and their daughter cells. Cell polarity can develop de novo, be maintained through rounds of cell division and be dynamically remodeled. In this Cell Science at a Glance review and poster, we describe molecular asymmetries that underlie cell polarity in several cellular contexts. We highlight multiple developmental systems that first establish cell/developmental polarity, and then maintain it. Our poster showcases repeated use of the Par, Scribble and Crumbs polarity complexes, which drive the development of cell polarity in many cell types and organisms. We then briefly discuss the diverse and dynamic changes in cell polarity that occur during cell migration, asymmetric cell division and in planar polarized tissues.
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Affiliation(s)
- Joseph P Campanale
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Thomas Y Sun
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Denise J Montell
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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20
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Klunder LJ, Faber KN, Dijkstra G, van IJzendoorn SCD. Mechanisms of Cell Polarity-Controlled Epithelial Homeostasis and Immunity in the Intestine. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a027888. [PMID: 28213466 DOI: 10.1101/cshperspect.a027888] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Intestinal epithelial cell polarity is instrumental to maintain epithelial homeostasis and balance communications between the gut lumen and bodily tissue, thereby controlling the defense against gastrointestinal pathogens and maintenance of immune tolerance to commensal bacteria. In this review, we highlight recent advances with regard to the molecular mechanisms of cell polarity-controlled epithelial homeostasis and immunity in the human intestine.
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Affiliation(s)
- Leon J Klunder
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
| | - Sven C D van IJzendoorn
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, the Netherlands
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21
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Kwan J, Sczaniecka A, Heidary Arash E, Nguyen L, Chen CC, Ratkovic S, Klezovitch O, Attisano L, McNeill H, Emili A, Vasioukhin V. DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2. Genes Dev 2017; 30:2696-2709. [PMID: 28087714 PMCID: PMC5238729 DOI: 10.1101/gad.284539.116] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
Abstract
Here, Kwan et al. investigated the mechanisms connecting cell polarity proteins with intracellular signaling pathways. They found that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, demonstrating a direct connection between cell polarity proteins and Hippo that is needed for proper development of multicellular organisms. Disruption of apical–basal polarity is implicated in developmental disorders and cancer; however, the mechanisms connecting cell polarity proteins with intracellular signaling pathways are largely unknown. We determined previously that membrane-associated guanylate kinase (MAGUK) protein discs large homolog 5 (DLG5) functions in cell polarity and regulates cellular proliferation and differentiation via undefined mechanisms. We report here that DLG5 functions as an evolutionarily conserved scaffold and negative regulator of Hippo signaling, which controls organ size through the modulation of cell proliferation and differentiation. Affinity purification/mass spectrometry revealed a critical role of DLG5 in the formation of protein assemblies containing core Hippo kinases mammalian ste20 homologs 1/2 (MST1/2) and Par-1 polarity proteins microtubule affinity-regulating kinases 1/2/3 (MARK1/2/3). Consistent with this finding, Hippo signaling is markedly hyperactive in mammalian Dlg5−/− tissues and cells in vivo and ex vivo and in Drosophila upon dlg5 knockdown. Conditional deletion of Mst1/2 fully rescued the phenotypes of brain-specific Dlg5 knockout mice. Dlg5 also interacts genetically with Hippo effectors Yap1/Taz. Mechanistically, we show that DLG5 inhibits the association between MST1/2 and large tumor suppressor homologs 1/2 (LATS1/2), uses its scaffolding function to link MST1/2 with MARK3, and inhibits MST1/2 kinase activity. These data reveal a direct connection between cell polarity proteins and Hippo, which is essential for proper development of multicellular organisms.
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Affiliation(s)
- Julian Kwan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anna Sczaniecka
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Emad Heidary Arash
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Liem Nguyen
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Chia-Chun Chen
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Srdjana Ratkovic
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Liliana Attisano
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Department of Pathology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington 98195, USA
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22
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Magro F, Gionchetti P, Eliakim R, Ardizzone S, Armuzzi A, Barreiro-de Acosta M, Burisch J, Gecse KB, Hart AL, Hindryckx P, Langner C, Limdi JK, Pellino G, Zagórowicz E, Raine T, Harbord M, Rieder F. Third European Evidence-based Consensus on Diagnosis and Management of Ulcerative Colitis. Part 1: Definitions, Diagnosis, Extra-intestinal Manifestations, Pregnancy, Cancer Surveillance, Surgery, and Ileo-anal Pouch Disorders. J Crohns Colitis 2017; 11:649-670. [PMID: 28158501 DOI: 10.1093/ecco-jcc/jjx008] [Citation(s) in RCA: 1156] [Impact Index Per Article: 165.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Fernando Magro
- Department of Pharmacology and Therapeutics, University of Porto; MedInUP, Centre for Drug Discovery and Innovative Medicines; Centro Hospitalar São João, Porto, Portugal
| | | | - Rami Eliakim
- Department of Gastroenterology and Hepatology, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sandro Ardizzone
- Gastrointestinal Unit ASST Fatebenefratelli Sacco-University of Milan-Milan, Italy
| | - Alessandro Armuzzi
- IBD Unit Complesso Integrato Columbus, Gastroenterological and Endocrino-Metabolical Sciences Department, Fondazione Policlinico Universitario Gemelli Universita' Cattolica del Sacro Cuore, Rome, Italy
| | - Manuel Barreiro-de Acosta
- Department of Gastroenterology, IBD Unit, University Hospital Santiago De Compostela (CHUS), A Coruña, Spain
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Krisztina B Gecse
- First Department of Medicine, Semmelweis University, Budapest,Hungary
| | | | - Pieter Hindryckx
- Department of Gastroenterology, University Hospital of Ghent, Ghent, Belgium
| | - Cord Langner
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Jimmy K Limdi
- Department of Gastroenterology, Pennine Acute Hospitals NHS Trust; Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Gianluca Pellino
- Unit of General Surgery, Second University of Naples,Napoli, Italy
| | - Edyta Zagórowicz
- Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Department of Oncological Gastroenterology Warsaw; Medical Centre for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Warsaw, Poland
| | - Tim Raine
- Department of Medicine, University of Cambridge, Cambridge,UK
| | - Marcus Harbord
- Imperial College London; Chelsea and Westminster Hospital, London,UK
| | - Florian Rieder
- Department of Pathobiology /NC22, Lerner Research Institute; Department of Gastroenterology, Hepatology and Nutrition/A3, Digestive Disease and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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23
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MacDonald TT, Di Sabatino A, DiSabatino A, Gordon JN. Immunopathogenesis of Crohn's Disease. JPEN J Parenter Enteral Nutr 2016; 29:S118-24; discussion S124-5, S184-8. [PMID: 15980273 DOI: 10.1177/01486071050290s4s118] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review highlights the huge advances made in the understanding of Crohn's disease in the last 15 years. The pathogenic immune response in the gut wall is a highly polarised T helper cell type 1 response, probably directed against antigens of the commensal flora. There is marked over-expression of pro-inflammatory cytokines such as tumor necrosis factor (TNF)-alpha and increased production of matrix degrading enzymes by fibroblasts and macrophages, which are probably responsible for ulceration and fistula formation. Crohn's disease runs in families and the susceptibility genes identified so far are associated with innate recognition of microbial products (Nod2) or epithelial barrier function (OCTN cation transporter genes and DLG5). Endogenous healing pathways mediated by transforming growth factor (TGF)-beta1 are inhibited because mucosal inflammatory cells express Smad7, the endogenous intracellular inhibitor of TGF-beta signalling. This makes it unlikely that enteral feeds containing TFG-beta are therapeutic by means of direct anti-inflammatory effects, however TGF-beta may still be involved because it is a well known epithelial motogen and may promote mucosal healing, in synergy with changes in mucosal bacterial populations as a result of the change in the diet.
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Affiliation(s)
- Thomas T MacDonald
- Division of Infection, Inflammation and Repair, University of Southampton School of Medicine, Southampton, United Kingdom.
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Wu Z, Qin W, Wu S, Zhu G, Bao W, Wu S. Identification of microRNAs regulating Escherichia coli F18 infection in Meishan weaned piglets. Biol Direct 2016; 11:59. [PMID: 27809935 PMCID: PMC5093996 DOI: 10.1186/s13062-016-0160-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022] Open
Abstract
Background Escherichia coli F18 is mainly responsible for post-weaning diarrhea (PWD) in piglets. The molecular regulation of E. coli F18 resistance in Chinese domestic weaned piglets is still obscure. We used Meishan piglets as model animals to test their susceptibility to E. coli F18. Small RNA duodenal libraries were constructed for E. coli F18-sensitive and -resistant weaned piglets challenged with E. coli F18 and sequenced using Illumina Solexa high-throughput sequencing technology. Results Sequencing results showed that 3,475,231 and 37,198,259 clean reads were obtained, with 311 known miRNAs differently expressed in resistant and sensitive groups, respectively. Twenty-four miRNAs, including 15 up-regulated and 9 down-regulated, demonstrated more than a 2-fold differential expression between the F18-resistant and -sensitive piglets. Stem-loop RT-qPCR showed that miR-136, miR-196b, miR-499-5p and miR-218-3p significantly expressed in intestinal tissue (p < 0.05). KEGG pathway analysis for target genes revealed that differently expressed miRNAs were involved in infectious diseases, signal transduction and immune system pathways. Interestingly, the expression of miR-218-3p in intestinal tissue had a very significant negative correlation with target DLG5 (P < 0.01). Conclusions Based on the expression correlation between miRNA and target genes analysis, we speculate that miR-218-3p targeting to DLG5, appears to be very promising candidate for miRNAs involved in response to E. coli F18 infection. The present study provides improved database information on pig miRNAs, better understanding of the genetic basis of E. coli F18 resistance in local Chinese pig breeds and lays a new foundation for identifying novel markers of E. coli F18 resistance. Reviewers This article was reviewed by Neil R Smalheiser and Weixiong Zhang. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0160-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Weiyun Qin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Seng Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China.
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Inflammatory bowel disease: exploring gut pathophysiology for novel therapeutic targets. Transl Res 2016; 176:38-68. [PMID: 27220087 DOI: 10.1016/j.trsl.2016.04.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 03/17/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
Ulcerative colitis and Crohn's disease are the 2 major phenotypes of inflammatory bowel disease (IBD), which are influenced by a complex interplay of immunological and genetic elements, though the precise etiology still remains unknown. With IBD developing into a globally prevailing disease, there is a need to explore new targets and a thorough understanding of the pathophysiological differences between the healthy and diseased gut could unearth new therapeutic opportunities. In this review, we provide an overview of the major aspects of IBD pathogenesis and thereafter present a comprehensive analysis of the gut pathophysiology leading to a discussion on some of the most promising targets and biologic therapies currently being explored. These include various gut proteins (CXCL-10, GATA-3, NKG2D, CD98, microRNAs), immune cells recruited to the gut (mast cells, eosinophils, toll-like receptors 2, 4), dysregulated proinflammatory cytokines (interleukin-6, -13, -18, -21), and commensal microbiota (probiotics and fecal microbiota transplantation). We also evaluate some of the emerging nonconventional therapies being explored in IBD treatment focusing on the latest developments in stem cell research, oral targeting of the gut-associated lymphoid tissue, novel anti-inflammatory signaling pathway targeting, adenosine deaminase inhibition, and the beneficial effects of antioxidant and nutraceutical therapies. In addition, we highlight the growth of biologics and their targets in IBD by providing information on the preclinical and clinical development of over 60 biopharmaceuticals representing the state of the art in ulcerative colitis and Crohn's disease drug development.
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Li X, Song P, Timofeeva M, Meng X, Rudan I, Little J, Satsangi J, Campbell H, Theodoratou E. Systematic meta-analyses and field synopsis of genetic and epigenetic studies in paediatric inflammatory bowel disease. Sci Rep 2016; 6:34076. [PMID: 27670835 PMCID: PMC5037432 DOI: 10.1038/srep34076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023] Open
Abstract
We provide a comprehensive field synopsis of genetic and epigenetic associations for paediatric Inflammatory Bowel Disease (IBD). A systematic review was performed and included 84 genetic association studies reporting data for 183 polymorphisms in 71 genes. Meta-analyses were conducted for 20 SNPs in 10 genes of paediatric Crohn’s disease (CD) and for 8 SNPs in 5 genes of paediatric ulcerative colitis (UC). Five epigenetic studies were also included, but formal meta-analysis was not possible. Venice criteria and Bayesian false discovery probability test were applied to assess the credibility of associations. Nine SNPs in 4 genes were considered to have highly credible associations with paediatric CD, of which four variants (rs2066847, rs12521868, rs26313667, rs1800629) were not previously identified in paediatric GWAS. Differential DNA methylation in NOD2 and TNF-α, dysregulated expression in let-7 and miR-124 were associated with paediatric IBD, but not as yet replicated. Highly credible SNPs associated with paediatric IBD have also been implicated in adult IBD, with similar magnitudes of associations. Early onset and distinct phenotypic features of paediatric IBD might be due to distinct epigenetic changes, but these findings need to be replicated. Further progress identifying genetic and epigenetic susceptibility of paediatric IBD will require international collaboration, population diversity and harmonization of protocols.
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Affiliation(s)
- Xue Li
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peige Song
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Xiangrui Meng
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh and Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Li Y, Chen P, Sun J, Huang J, Tie H, Li L, Li H, Ren G. Meta-analysis of associations between DLG5 R30Q and P1371Q polymorphisms and susceptibility to inflammatory bowel disease. Sci Rep 2016; 6:33550. [PMID: 27633114 PMCID: PMC5025715 DOI: 10.1038/srep33550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/30/2016] [Indexed: 01/01/2023] Open
Abstract
Growing evidence from recent studies has demonstrated an association between inflammatory bowel disease (IBD) susceptibility and two polymorphisms of DLG5 R30Q (rs1248696) and P1371Q (rs2289310), but the results remain controversial. We conducted a meta-analysis including a total of 22 studies with 10,878 IBD patients and 7917 healthy controls for R30Q and 5277 IBD cases and 4367 controls for P1371Q in order to systematically assess their association with the disease. The results indicated that R30Q was significantly associated with reduced susceptibility to IBD in Europeans by allelic and dominant comparisons, but not in overall population. No significant association was found between R30Q and Crohn's disease (CD) or ulcerative colitis (UC). P1371Q was associated with increased risk of IBD in Europeans and Americans. On the contrary, a decreased risk of IBD was observed in Asian population for P1371Q. In disease subgroup analysis, we found that P1371Q was also significantly associated with CD, but this relationship was not present for UC. In conclusion, our results strongly suggest that the both polymorphisms of DLG5 are correlated with IBD susceptibility in an ethnic-specific manner. Additional well-designed studies with large and diverse cohorts are needed to further strengthen our findings.
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Affiliation(s)
- Yunhai Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ping Chen
- Department of Rheumatology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Jiazheng Sun
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Huang
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hongtao Tie
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Liangliang Li
- Department of Rheumatology, Daping Hospital, Third Military Medical University, Chongqing, China
| | - Hongzhong Li
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guosheng Ren
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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A Genome-Wide Methylation Approach Identifies a New Hypermethylated Gene Panel in Ulcerative Colitis. Int J Mol Sci 2016; 17:ijms17081291. [PMID: 27517910 PMCID: PMC5000688 DOI: 10.3390/ijms17081291] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/26/2016] [Accepted: 08/03/2016] [Indexed: 12/12/2022] Open
Abstract
The cause of inflammatory bowel disease (IBD) is still unknown, but there is growing evidence that environmental factors such as epigenetic changes can contribute to the disease etiology. The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA methylation approach. Using an Infinium HumanMethylation450 BeadChip array, we screened the DNA methylation changes in three normal colon controls and eight UC patients. Using these methylation profiles, 48 probes associated with CpG promoter methylation showed differential hypermethylation between UC patients and normal controls. Technical validations for methylation analyses in a larger series of UC patients (n = 79) were performed by methylation-specific PCR (MSP) and bisulfite sequencing analysis. We finally found that three genes (FAM217B, KIAA1614 and RIBC2) that were significantly elevating the promoter methylation levels in UC compared to normal controls. Interestingly, we confirmed that three genes were transcriptionally silenced in UC patient samples by qRT-PCR, suggesting that their silencing is correlated with the promoter hypermethylation. Pathway analyses were performed using GO and KEGG databases with differentially hypermethylated genes in UC. Our results highlight that aberrant hypermethylation was identified in UC patients which can be a potential biomarker for detecting UC. Moreover, pathway-enriched hypermethylated genes are possibly implicating important cellular function in the pathogenesis of UC. Overall, this study describes a newly hypermethylated gene panel in UC patients and provides new clinical information that can be used for the diagnosis and therapeutic treatment of IBD.
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Metzger J, Pfahler S, Distl O. Variant detection and runs of homozygosity in next generation sequencing data elucidate the genetic background of Lundehund syndrome. BMC Genomics 2016; 17:535. [PMID: 27485430 PMCID: PMC4971756 DOI: 10.1186/s12864-016-2844-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/17/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Lundehund is a highly specialized breed characterized by a unique flexibility of the joints and polydactyly in all four limbs. The extremely small population size and high inbreeding has promoted a high frequency of diseased dogs affected by the Lundehund syndrome (LS), a severe gastro-enteropathic disease. RESULTS Comprehensive analysis of bead chip and whole-genome sequencing data for LS in the Lundehund resulted in a genome-wide association signal on CFA 34 and LS-specific runs of homozygosity (ROH) in this region. Filtering analysis for variants with predicted high or moderate effects revealed a missense mutation in LEPREL1 1.2 Mb proximal to the region of the genome-wide association, which was shown to be significantly associated with LS. LS-affected Lundehund harbored the mutant LEPREL1:g.139212C>G genotype A/A whereas all controls of other breeds showed the C/C wild type. In addition, ROH analysis for the Lundehund indicated a high enrichment of genes in potential signatures of selection affecting protein activation and immunoregulatory processes like NOD1 potentially involved in LS breed disposition. CONCLUSIONS Sequencing results for Lundehund specific traits reveal a potential causative mutation for LS in the neuropeptide operating gene LEPREL1 and suggests it as a precursor of the inflammatory process. Analyses of ROH regions give an insight into the genetic background of characteristic traits in the Lundehund that remain to be elucidated in the future.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover Foundation, Hanover, Germany.
| | - Sophia Pfahler
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover Foundation, Hanover, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover Foundation, Hanover, Germany
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Abstract
The intestinal microbiota has important metabolic and host-protective functions. Conversely to these beneficial functions, the intestinal microbiota is thought to play a central role in the etiopathogenesis of inflammatory bowel disease (IBD; Crohn's disease and ulcerative colitis), a chronic inflammation of the gut mucosa. Genetic screens and studies in experimental mouse models have clearly demonstrated that IBD can develop due to excessive translocation of bacteria into the bowel wall or dysregulated handling of bacteria in genetically susceptible hosts. In healthy individuals, the microbiota is efficiently separated from the mucosal immune system of the gut by the gut barrier, a single layer of highly specialized epithelial cells, some of which are equipped with innate immune functions to prevent or control access of bacterial antigens to the mucosal immune cells. It is currently unclear whether the composition of the microbial flora or individual bacterial strains or pathogens induces or supports the pathogenesis of IBD. Further research will be necessary to carefully dissect the contribution of individual bacterial species to this disease and to ascertain whether specific modulation of the intestinal microbiome may represent a valuable further option for future therapeutic strategies.
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Affiliation(s)
- Christoph Becker
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
| | - Markus F Neurath
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
| | - Stefan Wirtz
- Christoph Becker, PhD, is associated professor, Markus F. Neurath, MD, is director, and Stefan Wirtz, PhD, is senior scientist at the Department of Medicine 1 at the Friedrich-Alexander University Erlangen-Nuremberg in Erlangen, Germany
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RETRACTED ARTICLE: Mouse models of intestinal inflammation and cancer. Arch Toxicol 2016; 90:2109-2130. [DOI: 10.1007/s00204-016-1747-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
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Hong SN, Park C, Park SJ, Lee CK, Ye BD, Kim YS, Lee S, Chae J, Kim JI, Kim YH. Deep resequencing of 131 Crohn's disease associated genes in pooled DNA confirmed three reported variants and identified eight novel variants. Gut 2016; 65:788-96. [PMID: 25731871 DOI: 10.1136/gutjnl-2014-308617] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/27/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Genome wide association studies (GWAS) and meta-analyses for Crohn's disease (CD) have not fully explained the heritability of CD, suggesting that additional loci are yet to be found and that the known loci may contain high effect rare risk variants that have thus far gone undetected by GWAS. While the cost of deep sequencing remains too high to analyse many samples, targeted sequencing of pooled DNA samples allows the efficient and cost effective capture of all variations in a target region. DESIGN We performed pooled sequencing in 500 Korean CD cases and 1000 controls to evaluate the coding exon and 5' and 3' untranslated regions of 131 CD associated genes. The identified genetic variants were validated using genotyping in an independent set of 500 CD cases and 1000 controls. RESULTS Pooled sequencing identified 30 common/low single nucleotide variants (SNVs) in 12 genes and 3 rare SNVs in 3 genes. Our results confirmed a significant association of CD with the following previously reported risk loci: rs3810936 in TNFSF15 (OR=1.83, p<2.2×10(-16)), rs76418789 in IL23R (OR=0.47, p=1.14×10(-8)) and rs2241880 in ATG16L1 (OR=1.30, p=5.28×10(-6)). In addition, novel loci were identified in TNFSF8 (rs3181374, OR=1.53, p=1.03×10(-14)), BTNL2 (rs28362680, OR=1.47, p=9.67×10(-11)), HLA-DQA2 (rs3208181, OR=1.36, p=4.66×10(-6)), STAT3 (rs1053004, OR=1.29, p=2.07×10(-5)), NFKBIA (rs2273650, OR=0.80, p=3.93×10(-4)), NKX2-3 (rs888208, OR=0.82, p=6.37×10(-4)) and DNAH12 (rs4462937, OR=1.13, p=3.17×10(-2)). A novel rare SNV, rs200735402 in CARD9, was shown to have a protective effect (OR=0.09, p=5.28×10(-5)). CONCLUSIONS Our deep resequencing of 131 CD associated genes confirmed 3 reported risk loci and identified 8 novel risk loci for CD in Koreans, providing new insights into the genetic architecture of CD.
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Affiliation(s)
- Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Changho Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Soo Jung Park
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Kyun Lee
- Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Centre, University of Ulsan College of Medicine
| | - You Sun Kim
- Department of Internal Medicine, Seoul Paik Hospital, Inje University College of Medicine, Seoul, Korea
| | - Seungbok Lee
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, Seoul, Korea
| | - Jeesoo Chae
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea Medical Research Center, Genomic Medicine Institute (GMI), Seoul National University, Seoul, Korea Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Sim S, Hibberd ML. Caenorhabditis elegans susceptibility to gut Enterococcus faecalis infection is associated with fat metabolism and epithelial junction integrity. BMC Microbiol 2016; 16:6. [PMID: 26769134 PMCID: PMC4714453 DOI: 10.1186/s12866-016-0624-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/08/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Gut bacteria-host interactions have been implicated in the pathogenesis of numerous human diseases, but few mechanisms have been described. The genetically tractable nematode worm Caenorhabditis elegans can be infected with pathogenic bacteria, such as the human gut commensal Enterococcus faecalis, via feeding, making it a good model for studying these interactions. RESULTS An RNAi screen of 17 worm candidate genes revealed that knockdown of the transcription factor nhr-49, a master regulator of fat metabolism, shortens worm lifespan upon infection with E. faecalis (and other potentially pathogenic bacteria) compared to Escherichia coli. The functional similarity of nhr-49 to the mammalian peroxisome proliferator-activated receptors (PPARs) suggests that this is mediated through a link between fatty acid metabolism and innate immunity. In addition, knockdown of either dlg-1 or ajm-1, which encode physically interacting proteins in the C. elegans epithelial junction, also reduces worm lifespan upon E. faecalis challenge, demonstrating the importance of the intestinal epithelium as an immune barrier. CONCLUSIONS The protective roles identified for nhr-49, dlg-1, and ajm-1 suggest mechanistic interactions between the gut microbiota, host fatty acid metabolism, innate immunity, and epithelial junction integrity that are remarkably similar to those implicated in human metabolic and inflammatory diseases.
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Affiliation(s)
- Shuzhen Sim
- Infectious Diseases, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.
| | - Martin L Hibberd
- Infectious Diseases, Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore, 138672, Singapore.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
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Kumar M, Hemalatha R, Nagpal R, Singh B, Parasannanavar D, Verma V, Kumar A, Marotta F, Catanzaro R, Cuffari B, Jain S, Bissi L, Yadav H. PROBIOTIC APPROACHES FOR TARGETING INFLAMMATORY BOWEL DISEASE: AN UPDATE ON ADVANCES AND OPPORTUNITIES IN MANAGING THE DISEASE. INTERNATIONAL JOURNAL OF PROBIOTICS & PREBIOTICS 2016; 11:99-116. [PMID: 31452650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 09/28/2022]
Abstract
Various commensal enteric and pathogenic bacteria may be involved in the pathogenesis of inflammatory bowel diseases (IBDs), a chronic condition with a pathogenic background that involves both immunogenetic and environmental factors. IBDs comprising of Crohn's disease, and ulcerative colitis, and pauchitis are chronic inflammatory conditions, and known for causing disturbed homeostatic balance among the intestinal immune compartment, gut epithelium and microbiome. An increasing trend of IBDs in incidence, prevalence, and severity has been reported during recent years. Probiotic strains have been reported to manage the IBDs and related pathologies, and hence are current hot topics of research for their potential to manage metabolic diseases as well as various immunopathologies. However, the probiotics industry will need to undergo a transformation, with increased focus on stringent manufacturing guidelines and high-quality clinical trials. This article reviews the present state of art of role of probiotic bacteria in reducing inflammation and strengthening the host immune system with reference to the management of IBDs. We infer that t healthcare will move beyond its prevailing focus on human physiology, and embrace the superorganism as a paradigm to understand and ameliorate IBDs.
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Affiliation(s)
- Manoj Kumar
- Department of Microbiology and Immunology, National Institute of Nutrition, Hyderabad
| | - Rajkumar Hemalatha
- Department of Microbiology and Immunology, National Institute of Nutrition, Hyderabad
| | - Ravinder Nagpal
- Probiotics Research Laboratory, Graduate School of Medicine, Juntendo University, Tokyo
| | - Birbal Singh
- Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Devraj Parasannanavar
- Department of Microbiology and Immunology, National Institute of Nutrition, Hyderabad
| | - Vinod Verma
- Centre of Biotechnology, Nehru Science Complex, University of Allahabad, Allahabad, India
| | - Ashok Kumar
- Department of Zoology, M.L.K. Post-Graduate College, Balrampur (U.P.), India
| | - Francesco Marotta
- ReGenera Research Group for Aging Intervention & MMC-Milano Medical, Milano, Italy
| | - Roberto Catanzaro
- Department of Internal Medicine, University of Catania, Catania, Italy
| | - Biagio Cuffari
- Department of Internal Medicine, University of Catania, Catania, Italy
| | - Shalini Jain
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura Bissi
- ReGenera Research Group for Aging Intervention & MMC-Milano Medical, Milano, Italy
| | - Hariom Yadav
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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Abstract
PURPOSE OF REVIEW Genome-wide association studies (GWAS) have helped to understand the genetic basis and pathogenesis of inflammatory bowel disease (IBD). However, understanding the functional and clinical consequences of the associated alleles has not followed the same pace. In this review, we discuss how studying the genetic predisposition to IBD has increased our understanding about IBD pathogenesis and how epigenetics is becoming more and more important. We describe the potential clinical applications of genetics, and provide important challenges in the field and the future steps to be taken. RECENT FINDINGS GWAS and meta-analyses have identified 163 loci associated with IBD, and have implicated key pathways in IBD pathogenesis. Only few of the association signals correspond to nonsynonymous coding variation with a clear effect on protein function. The majority of signals involve noncoding genetic variation, of which a large part is related to gene expression changes. More recently, expression and epigenetic studies in IBD are increasingly being reported, and have shown that many effects seem to be highly cell-type specific.Predictive genetic testing will not be for the immediate future for the majority of IBD patients. However, for the subset of patients with very-early onset IBD, several causal mutations have been found. Predictive genetic panels for these adolescents presenting with a very severe disease course, and/or families with high penetrance of disease will be of benefit. SUMMARY Genetic, transcriptomic and epigenetic studies have offered exciting clues about IBD pathogenesis but are unlikely to provide all answers. To fully grasp the function of disease-associated genetic variants, identifying causal genes and translating this knowledge into predictive biomarkers and new treatments, we should now integrate all these disciplines.
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Can inflammatory bowel disease really be solved by the multiple -omics and meta-omics analyses? Immunol Lett 2015; 165:107-8. [PMID: 25827759 DOI: 10.1016/j.imlet.2015.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022]
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Central role of gimap5 in maintaining peripheral tolerance and T cell homeostasis in the gut. Mediators Inflamm 2015; 2015:436017. [PMID: 25944983 PMCID: PMC4405212 DOI: 10.1155/2015/436017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/15/2014] [Indexed: 01/01/2023] Open
Abstract
Inflammatory bowel disease (IBD) including Crohn's disease and ulcerative colitis is often precipitated by an abnormal immune response to microbiota due to host genetic aberrancies. Recent studies highlight the importance of the host genome and microflora interactions in the pathogenesis of mucosal inflammation including IBD. Specifically, genome-wide (GWAS) and also next-generation sequencing (NGS)—including whole exome or genome sequencing—have uncovered a large number of susceptibility loci that predispose to autoimmune diseases and/or the two phenotypes of IBD. In addition, the generation of “IBD-prone” animal models using both reverse and forward genetic approaches has not only helped confirm the identification of susceptibility loci but also shed critical insight into the underlying molecular and cellular pathways that drive colitis development. In this review, we summarize recent findings derived from studies involving a novel early-onset model of colitis as it develops in GTPase of immunity-associated protein 5- (Gimap5-) deficient mice. In humans, GIMAP5 has been associated with autoimmune diseases although its function is poorly defined. Here, we discuss how defects in Gimap5 function impair immunological tolerance and lymphocyte survival and ultimately drive the development of CD4+ T cell-mediated early-onset colitis.
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Chua KH, Lian LH, Khor WC, Lee WS, Hilmi I, Goh KL, Kee BP. Association between genetic polymorphisms in interferon regulatory factor 5 (IRF5) gene and Malaysian patients with Crohn's disease. J Dig Dis 2015; 16:205-16. [PMID: 25564941 DOI: 10.1111/1751-2980.12229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The study aimed to investigate the association between the interferon regulatory factor 5 (IRF5) gene polymorphisms and the onset of Crohn's disease (CD) in a Malaysian cohort. METHODS Genomic DNA was extracted from blood samples collected from 91 CD patients and 100 healthy individuals via a conventional phenol-chloroform extraction method. Screening of the four target single nucleotide polymorphisms (SNPs), including rs3807306, rs4728142, rs10954213 and rs11770589 was carried out in a real-time polymerase chain reaction (PCR) thermal cycler using TaqMan genotyping assay. The genetic data obtained was subsequently subjected to statistical analysis to relate the SNPs to the onset of CD in the Malaysian population. The genotyping assay and data were further validated selectively by conventional PCR amplification of the SNP sites and DNA sequencing. RESULTS The rs3807306 G allele was a risk factor for CD (OR 2.3630, P = 0.00004), whereas the homozygous T genotype was protective against the disease (OR 0.2038, P = 0.00004). The heterozygous A/G genotype of rs10954213 was significantly associated with CD (OR 4.319, P = 0.0377). On the other hand, the homozygous A and heterozygous A/G genotypes of the rs11770589 were significant in the controls (OR 0.4242, P = 0.0166) and patients (OR 2.000, P = 0.0179), respectively. In the ethnic-stratification analysis, the rs11770589 homozygous A genotype was protective in Indians (OR 0.1551, P = 0.0112). CONCLUSION IRF5 gene polymorphisms may play a role in the development of CD in the Malaysian population.
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Affiliation(s)
- Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Determinants of intestinal permeability in healthy first-degree relatives of individuals with Crohn's disease. Inflamm Bowel Dis 2015; 21:879-87. [PMID: 25734694 DOI: 10.1097/mib.0000000000000323] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The Genetics, Environmental, Microbial Project is a multicenter study assessing etiological factors in Crohn's disease by studying healthy first-degree relatives (FDRs) of individuals affected by Crohn's disease. We aimed to evaluate the contribution of genetic, microbial, and environmental factors to the determination of intestinal permeability in healthy FDRs. METHODS IP was assessed using the lactulose-mannitol ratio (LacMan ratio). FDRs were genotyped for 167 inflammatory bowel disease-associated single nucleotide polymorphisms. Taxonomic profile of the fecal microbiota was determined by Illumina MiSeq pyrosequencing of 16S ribosomal RNA. The associations of LacMan ratio with demographic factors, inflammatory bowel disease-associated single nucleotide polymorphisms and the fecal microbiota were assessed. RESULTS One thousand, one hundred ninety-six white FDRs were included [corrected]. Eleven percent of FDRs had an elevated LacMan ratio (≥0.03). A multivariate analysis demonstrated that younger subjects and nonsmokers had higher LacMan ratios, P = 3.62 × 10⁻⁴ and P = 0.03, respectively. The LacMan ratio was not significantly heritable, H2r, 0.13, P = 0.13. There was no association between any of the 167 inflammatory bowel disease-associated risk variants and LacMan ratio nor was there a correlation between fecal microbial composition and the LacMan ratio. CONCLUSIONS We did not find LacMan ratio to be significantly heritable suggesting that the contribution of genetic factors to the determination of intestinal permeability in healthy FDRs is modest. Environmental factors, such as smoking, are likely more important determinants. The effect of age on intestinal barrier function has been underappreciated.
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Lin WH, Asmann YW, Anastasiadis PZ. Expression of polarity genes in human cancer. Cancer Inform 2015; 14:15-28. [PMID: 25991909 PMCID: PMC4390136 DOI: 10.4137/cin.s18964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 01/01/2023] Open
Abstract
Polarity protein complexes are crucial for epithelial apical–basal polarity and directed cell migration. Since alterations of these processes are common in cancer, polarity proteins have been proposed to function as tumor suppressors or oncogenic promoters. Here, we review the current understanding of polarity protein functions in epithelial homeostasis, as well as tumor formation and progression. As most previous studies focused on the function of single polarity proteins in simplified model systems, we used a genomics approach to systematically examine and identify the expression profiles of polarity genes in human cancer. The expression profiles of polarity genes were distinct in different human tissues and classified cancer types. Additionally, polarity expression profiles correlated with disease progression and aggressiveness, as well as with identified cancer types, where specific polarity genes were commonly altered. In the case of Scribble, gene expression analysis indicated its common amplification and upregulation in human cancer, suggesting a tumor promoting function.
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Affiliation(s)
- Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL, USA
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Discs large 5, an Essential Gene in Drosophila, Regulates Egg Chamber Organization. G3-GENES GENOMES GENETICS 2015; 5:943-52. [PMID: 25795662 PMCID: PMC4426378 DOI: 10.1534/g3.115.017558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Discs large 5 (Dlg5) is a member of the MAGUK family of proteins that typically serve as molecular scaffolds and mediate signaling complex formation and localization. In vertebrates, Dlg5 has been shown to be responsible for polarization of neural progenitors and to associate with Rab11-positive vesicles in epithelial cells. In Drosophila, however, the function of Dlg5 is not well-documented. We have identified dlg5 as an essential gene that shows embryonic lethality. dlg5 embryos display partial loss of primordial germ cells (PGCs) during gonad coalescence between stages 12 and 15 of embryogenesis. Loss of Dlg5 in germline and somatic stem cells in the ovary results in the depletion of both cell lineages. Reduced expression of Dlg5 in the follicle cells of the ovary leads to a number of distinct phenotypes, including defects in egg chamber budding, stalk cell overgrowth, and ectopic polar cell induction. Interestingly, loss of Dlg5 in follicle cells results in abnormal distribution of a critical component of cell adhesion, E-cadherin, shown to be essential for proper organization of egg chambers.
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Dignass A, Eliakim R, Magro F, Maaser C, Chowers Y, Geboes K, Mantzaris G, Reinisch W, Colombel JF, Vermeire S, Travis S, Lindsay JO, van Assche G. [Second European evidence-based Consensus on the diagnosis and management of ulcerative colitis Part 1: Definitions and diagnosis (Spanish version)]. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2014; 79:263-89. [PMID: 25487134 DOI: 10.1016/j.rgmx.2014.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 10/23/2014] [Indexed: 02/07/2023]
Affiliation(s)
- A Dignass
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo.
| | - R Eliakim
- AD y RE contribuyeron de igual manera en este trabajo
| | - F Magro
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - C Maaser
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - Y Chowers
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - K Geboes
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - G Mantzaris
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - W Reinisch
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - J-F Colombel
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - S Vermeire
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - S Travis
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - J O Lindsay
- AD y GVA actuaron como coordinadores del Consenso; AD y RE contribuyeron de igual manera en este trabajo
| | - G van Assche
- AD y GVA actuaron como coordinadores del Consenso.
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Zhou Z, Guo Y, Liu Y, Zhang F, Wang Y, Shen B, Qin Y, Qiu J. Methylation-mediated silencing of Dlg5 facilitates bladder cancer metastasis. Exp Cell Res 2014; 331:399-407. [PMID: 25478998 DOI: 10.1016/j.yexcr.2014.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED Dlg5 (Discs large homolog 5), a member of the membrane-associated guanylate kinase adaptor family of scaffolding proteins, has been shown to participate in cancer progression. However, little is known about whether abnormal expression of Dlg5 facilitates bladder cancer metastasis. In the current study we initiated a study analyzing Dlg5 expression and its roles in human bladder cancer metastasis. The expression of Dlg5 is decreased in most bladder cancer tissues compared with adjacent normal tissues, and Dlg5 expression is further downregulated in patients with muscle-invasive tumors. DNA methylation analysis showed a methylation of Dlg5 gene in bladder cancer cell lines and in bladder cancer tumors, especially in muscle-invasive tumors. Hypermethylation of Dlg5 in bladder tumors is tightly correlated with silencing of Dlg5 expression, which is further functionally validated by demethylation analysis in bladder cancer cell lines. Knockdown of Dlg5 increases cancer cell invasion in vitro and promotes cancer metastasis in vivo. Of clinical significance, Kaplan-Meier analysis showed that downregulation of Dlg5 is significantly associated with reduced overall survival in patients with bladder cancer. CONCLUSION These data suggest that inhibition of Dlg5 by DNA hypermethylation contributes to provoke invasive phenotypes in bladder tumor.
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Affiliation(s)
- Zhihua Zhou
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Yifeng Guo
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Yong Liu
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Fang Zhang
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Yong Wang
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Bing Shen
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Yan Qin
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China
| | - Jianxin Qiu
- Department of Urology, Shanghai First People׳s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200008, China.
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Potentially functional SNPs (pfSNPs) as novel genomic predictors of 5-FU response in metastatic colorectal cancer patients. PLoS One 2014; 9:e111694. [PMID: 25372392 PMCID: PMC4221105 DOI: 10.1371/journal.pone.0111694] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/29/2014] [Indexed: 12/31/2022] Open
Abstract
5-Fluorouracil (5-FU) and its pro-drug Capecitabine have been widely used in treating colorectal cancer. However, not all patients will respond to the drug, hence there is a need to develop reliable early predictive biomarkers for 5-FU response. Here, we report a novel potentially functional Single Nucleotide Polymorphism (pfSNP) approach to identify SNPs that may serve as predictive biomarkers of response to 5-FU in Chinese metastatic colorectal cancer (CRC) patients. 1547 pfSNPs and one variable number tandem repeat (VNTR) in 139 genes in 5-FU drug (both PK and PD pathway) and colorectal cancer disease pathways were examined in 2 groups of CRC patients. Shrinkage of liver metastasis measured by RECIST criteria was used as the clinical end point. Four non-responder-specific pfSNPs were found to account for 37.5% of all non-responders (P<0.0003). Five additional pfSNPs were identified from a multivariate model (AUC under ROC = 0.875) that was applied for all other pfSNPs, excluding the non-responder-specific pfSNPs. These pfSNPs, which can differentiate the other non-responders from responders, mainly reside in tumor suppressor genes or genes implicated in colorectal cancer risk. Hence, a total of 9 novel SNPs with potential functional significance may be able to distinguish non-responders from responders to 5-FU. These pfSNPs may be useful biomarkers for predicting response to 5-FU.
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Dave M, Papadakis KA, Faubion WA. Immunology of inflammatory bowel disease and molecular targets for biologics. Gastroenterol Clin North Am 2014; 43:405-24. [PMID: 25110250 PMCID: PMC4480636 DOI: 10.1016/j.gtc.2014.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Inflammatory bowel disease (IBD) is an immune-mediated disease and involves a complex interplay of host genetics and environmental influences. Recent advances in the field, including data from genome-wide association studies and microbiome analysis, have started to unravel the complex interaction between host genetics and environmental influences in the pathogenesis of IBD. A drawback of current clinical trials is inadequate or lack of immune phenotyping of patients. However, recent advances in high-throughput technologies provide an opportunity to monitor the dynamic and complex immune system, which may to lead to a more personalized treatment approach in IBD.
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Ngo ST, Steyn FJ, McCombe PA. Gender differences in autoimmune disease. Front Neuroendocrinol 2014; 35:347-69. [PMID: 24793874 DOI: 10.1016/j.yfrne.2014.04.004] [Citation(s) in RCA: 604] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/20/2014] [Accepted: 04/22/2014] [Indexed: 12/21/2022]
Abstract
Autoimmune diseases are a range of diseases in which the immune response to self-antigens results in damage or dysfunction of tissues. Autoimmune diseases can be systemic or can affect specific organs or body systems. For most autoimmune diseases there is a clear sex difference in prevalence, whereby females are generally more frequently affected than males. In this review, we consider gender differences in systemic and organ-specific autoimmune diseases, and we summarize human data that outlines the prevalence of common autoimmune diseases specific to adult males and females in countries commonly surveyed. We discuss possible mechanisms for sex specific differences including gender differences in immune response and organ vulnerability, reproductive capacity including pregnancy, sex hormones, genetic predisposition, parental inheritance, and epigenetics. Evidence demonstrates that gender has a significant influence on the development of autoimmune disease. Thus, considerations of gender should be at the forefront of all studies that attempt to define mechanisms that underpin autoimmune disease.
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Affiliation(s)
- S T Ngo
- School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia; University of Queensland Centre for Clinical Research, University of Queensland, Herston, Queensland, Australia
| | - F J Steyn
- School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia
| | - P A McCombe
- University of Queensland Centre for Clinical Research, University of Queensland, Herston, Queensland, Australia; Department of Neurology, Royal Brisbane & Women's Hospital, Herston, Queensland, Australia.
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Tawfik A, Flanagan PK, Campbell BJ. Escherichia coli-host macrophage interactions in the pathogenesis of inflammatory bowel disease. World J Gastroenterol 2014; 20:8751-8763. [PMID: 25083050 PMCID: PMC4112894 DOI: 10.3748/wjg.v20.i27.8751] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/07/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
Multiple studies have demonstrated alterations in the intestinal microbial community (termed the microbiome) in Crohn’s disease (CD) and several lines of evidence suggest these changes may have a significant role in disease pathogenesis. In active and quiescent disease, both the faecal and mucosa-associated microbiome are discordant with matched controls with reduced biodiversity, changes in dominant organisms and increased temporal variation described. Mucosa-associated adherent, invasive Escherichia coli (E. coli) (AIEC), pro-inflammatory and resistant to killing by mucosal macrophages, appear to be particularly important. AIEC possess several virulence factors which may confer pathogenic potential in CD. Type-1 pili (FimH) allow adherence to intestinal cells via cell-surface carcinoembryonic antigen-related cell adhesion molecules and possession of long polar fimbrae promotes translocation across the intestinal mucosa via microfold (M)-cells of the follicle-associated epithelium. Resistance to stress genes (htrA, dsbA and hfq) and tolerance of an acidic pH may contribute to survival within the phagolysosomal environment. Here we review the current understanding of the role of mucosa-associated E. coli in Crohn’s pathogenesis, the role of the innate immune system, factors which may contribute to prolonged bacterial survival and therapeutic strategies to target intracellular E. coli.
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Liu JZ, Anderson CA. Genetic studies of Crohn's disease: past, present and future. Best Pract Res Clin Gastroenterol 2014; 28:373-86. [PMID: 24913378 PMCID: PMC4075408 DOI: 10.1016/j.bpg.2014.04.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/14/2014] [Accepted: 04/24/2014] [Indexed: 01/31/2023]
Abstract
The exact aetiology of Crohn's disease is unknown, though it is clear from early epidemiological studies that a combination of genetic and environmental risk factors contributes to an individual's disease susceptibility. Here, we review the history of gene-mapping studies of Crohn's disease, from the linkage-based studies that first implicated the NOD2 locus, through to modern-day genome-wide association studies that have discovered over 140 loci associated with Crohn's disease and yielded novel insights into the biological pathways underlying pathogenesis. We describe on-going and future gene-mapping studies that utilise next generation sequencing technology to pinpoint causal variants and identify rare genetic variation underlying Crohn's disease risk. We comment on the utility of genetic markers for predicting an individual's disease risk and discuss their potential for identifying novel drug targets and influencing disease management. Finally, we describe how these studies have shaped and continue to shape our understanding of the genetic architecture of Crohn's disease.
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Affiliation(s)
- Jimmy Z Liu
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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