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Simovic I, Hilmi I, Ng RT, Chew KS, Wong SY, Lee WS, Riordan S, Castaño-Rodríguez N. ATG16L1 rs2241880/T300A increases susceptibility to perianal Crohn's disease: An updated meta-analysis on inflammatory bowel disease risk and clinical outcomes. United European Gastroenterol J 2024; 12:103-121. [PMID: 37837511 PMCID: PMC10859713 DOI: 10.1002/ueg2.12477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/17/2023] [Indexed: 10/16/2023] Open
Abstract
BACKGROUND ATG16L1 plays a fundamental role in the degradative intracellular pathway known as autophagy, being a mediator of inflammation and microbial homeostasis. The variant rs2241880 can diminish these capabilities, potentially contributing to inflammatory bowel disease (IBD) pathogenesis. OBJECTIVES To perform an updated meta-analysis on the association between ATG16L1 rs2241880 and IBD susceptibility by exploring the impact of age, ethnicity, and geography. Moreover, to investigate the association between rs2241880 and clinical features. METHODS Literature searches up until September 2022 across 7 electronic public databases were performed for all case-control studies on ATG16L1 rs2241880 and IBD. Pooled odds ratios (ORP ) and 95% CI were calculated under the random effects model. RESULTS Our analyses included a total of 30,606 IBD patients, comprising 21,270 Crohn's disease (CD) and 9336 ulcerative colitis (UC) patients, and 33,329 controls. ATG16L1 rs2241880 was significantly associated with CD susceptibility, where the A allele was protective (ORP : 0.74, 95% CI: 0.72-0.77, p-value: <0.001), while the G allele was a risk factor (ORP : 1.23, 95% CI: 1.09-1.39, p-value: 0.001), depending on the minor allele frequencies observed in this multi-ancestry study sample. rs2241880 was predominantly relevant in Caucasians from North America and Europe, and in Latin American populations. Importantly, CD patients harbouring the G allele were significantly more predisposed to perianal disease (ORP : 1.21, 95% CI: 1.07-1.38, p-value: 0.003). CONCLUSIONS ATG16L1 rs2241880 (G allele) is a consistent risk factor for IBD in Caucasian cohorts and influences clinical outcomes. As its role in non-Caucasian populations remains ambiguous, further studies in under-reported populations are necessary.
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Affiliation(s)
- Isidora Simovic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Ruey Terng Ng
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Shin Yee Wong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Way Seah Lee
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Stephen Riordan
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Kuala Lumpur, Malaysia
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Sosna B, Aebisher D, Myśliwiec A, Dynarowicz K, Bartusik-Aebisher D, Oleś P, Cieślar G, Kawczyk-Krupka A. Selected Cytokines and Metalloproteinases in Inflammatory Bowel Disease. Int J Mol Sci 2023; 25:202. [PMID: 38203373 PMCID: PMC10779120 DOI: 10.3390/ijms25010202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a collective term for two diseases: ulcerative colitis (UC) and Crohn's disease (CD). There are many factors, e.g., genetic, environmental and immunological, that increase the likelihood of these diseases. Indicators of IBDs include extracellular matrix metalloproteinases (MMPs). The aim of this review is to present data on the role of selected cytokines and metalloproteinases in IBD. In recent years, more and more transcriptomic studies are emerging. These studies are improving the characterization of the cytokine microenvironment inside inflamed tissue. It is observed that the levels of several cytokines are consistently increased in inflamed tissue in IBD, both in UC and CD. This review shows that MMPs play a major role in the pathology of inflammatory processes, cancer, and IBD. IBD-associated inflammation is associated with increased expression of MMPs and reduced ability of tissue inhibitors of metalloproteinases (TIMPs) to inhibit their action. In IBD patients in tissues that are inflamed, MMPs are produced in excess and TIMP activity is not sufficient to block MMPs. This review is based on our personal selection of the literature that was retrieved by a selective search in PubMed using the terms "Inflammatory bowel disease" and "pathogenesis of Inflammatory bowel diseases" that includes systematic reviews, meta-analyses, and clinical trials. The involvement of the immune system in the pathophysiology of IBD is reviewed in terms of the role of the cytokines and metalloproteinases involved.
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Affiliation(s)
- Barbara Sosna
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - David Aebisher
- Department of Photomedicine and Physical Chemistry, Medical College, University of Rzeszów, 35-959 Rzeszów, Poland;
| | - Angelika Myśliwiec
- Center for Innovative Research in Medical and Natural Sciences, Medical College, University of Rzeszów, 35-310 Rzeszów, Poland; (A.M.); (K.D.)
| | - Klaudia Dynarowicz
- Center for Innovative Research in Medical and Natural Sciences, Medical College, University of Rzeszów, 35-310 Rzeszów, Poland; (A.M.); (K.D.)
| | - Dorota Bartusik-Aebisher
- Department of Biochemistry and General Chemistry, Medical College, University of Rzeszów, 35-959 Rzeszów, Poland;
| | - Piotr Oleś
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - Grzegorz Cieślar
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
| | - Aleksandra Kawczyk-Krupka
- Department of Internal Medicine, Angiology and Physical Medicine, Center for Laser Diagnostics and Therapy, Medical University of Silesia in Katowice, Batorego 15 Street, 41-902 Bytom, Poland; (B.S.); (P.O.); (G.C.)
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Khatiwada A, Yilmaz AS, Wolf BJ, Pietrzak M, Chung D. multi-GPA-Tree: Statistical approach for pleiotropy informed and functional annotation tree guided prioritization of GWAS results. PLoS Comput Biol 2023; 19:e1011686. [PMID: 38060592 PMCID: PMC10729974 DOI: 10.1371/journal.pcbi.1011686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 12/19/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), most with small or moderate effect sizes, making them difficult to detect. Second, many complex traits share a common genetic basis due to 'pleiotropy' and and though few methods consider it, leveraging pleiotropy can improve statistical power to detect genotype-trait associations with weaker effect sizes. Third, currently available statistical methods are limited in explaining the functional mechanisms through which genetic variants are associated with specific or multiple traits. We propose multi-GPA-Tree to address these challenges. The multi-GPA-Tree approach can identify risk SNPs associated with single as well as multiple traits while also identifying the combinations of functional annotations that can explain the mechanisms through which risk-associated SNPs are linked with the traits. First, we implemented simulation studies to evaluate the proposed multi-GPA-Tree method and compared its performance with existing statistical approaches. The results indicate that multi-GPA-Tree outperforms existing statistical approaches in detecting risk-associated SNPs for multiple traits. Second, we applied multi-GPA-Tree to a systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and to a Crohn's disease (CD) and ulcertive colitis (UC) GWAS, and functional annotation data including GenoSkyline and GenoSkylinePlus. Our results demonstrate that multi-GPA-Tree can be a powerful tool that improves association mapping while facilitating understanding of the underlying genetic architecture of complex traits and potential mechanisms linking risk-associated SNPs with complex traits.
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Affiliation(s)
- Aastha Khatiwada
- Department of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, United States of America
| | - Ayse Selen Yilmaz
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
| | - Bethany J. Wolf
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
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Ajayi T, Rai P, Shi M, Gabor KA, Karmaus PWF, Meacham JM, Katen K, Madenspacher JH, Schurman SH, Fessler MB. Race-specific association of an IRGM risk allele with cytokine expression in human subjects. Sci Rep 2023; 13:12911. [PMID: 37558924 PMCID: PMC10412543 DOI: 10.1038/s41598-023-40313-3] [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: 05/30/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Immunity-related GTPase family M (IRGM), located on human chromosome 5q33.1, encodes a protein that promotes autophagy and suppresses the innate immune response. The minor allele of rs13361189 (-4299T>C), a single nucleotide polymorphism in the IRGM promoter, has been associated with several diseases, including Crohn's disease and tuberculosis. Although patterns of linkage disequilibrium and minor allele frequency for this polymorphism differ dramatically between subjects of European and African descent, studies of rs13361189 have predominantly been conducted in Europeans and the mechanism of association is poorly understood. We recruited a cohort of 68 individuals (30 White, 34 African American, 4 other race) with varying rs13361189 genotypes and assessed a panel of immune response measures including whole blood cytokine induction following ex vivo stimulation with Toll-like Receptor ligands. Minor allele carriers were found to have increased serum immunoglobulin M, C-reactive protein, and circulating CD8+ T cells. No differences in whole blood cytokines were observed between minor allele carriers and non-carriers in the overall study population; however, minor allele status was associated with increased induction of a subset of cytokines among African American subjects, and decreased induction among White subjects. These findings underline the importance of broad racial inclusion in genetic studies of immunity.
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Affiliation(s)
- Teminioluwa Ajayi
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Prashant Rai
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Min Shi
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Kristin A Gabor
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Peer W F Karmaus
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Julie M Meacham
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Kevin Katen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jennifer H Madenspacher
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Shepherd H Schurman
- Clinical Research Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
- Clinical Research Unit, National Institute on Aging, Baltimore, MD, 21225, USA
| | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, MD D2-01, P.O. Box 12233, Research Triangle Park, NC, 27709, USA.
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Zhang H, Ni Y, Ji H, Liu H, Liu S. Research trends of omics in ulcerative colitis: A bibliometric analysis. Front Med (Lausanne) 2023; 10:1115240. [PMID: 37051213 PMCID: PMC10083299 DOI: 10.3389/fmed.2023.1115240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/20/2023] [Indexed: 03/28/2023] Open
Abstract
BackgroundOmics has emerged as a promising biological science to shed light on the etiology, pathogenesis, and treatment of ulcerative colitis (UC). At present, although research on the omics of UC has drawn global attention, there is still a lack of bibliometric analysis in this field. This study aimed to access the trends and hotspots of omics in UC research.MethodPublications related to omics in UC from 1 January 2000 to 15 October 2022 were retrieved from the Web of Science Core Collection database. VOSviewer, CiteSpace, and the online bibliometric analysis platform “Bibliometrix” were adopted to extract and visualize information.ResultsA total of 385 publications were finally included and the annual number of publications fluctuated. The trend in publications increased rapidly after 2019. The United States showed its dominant position in several publications, total citations, and international collaborations. The top five research organizations for publications on the research of omics in UC were Harvard Medical School, the Icahn School of Medicine at Mount Sinai, Karolinska Institutet, the Brigham and Women's Hospital, and the Massachusetts General Hospital. Ashwin Ananthakrishnan from the Massachusetts General Hospital was the most productive author, and Séverine Vermeire from the Catholic University of Leuven was co-cited most often. Inflammatory bowel disease was the most popular and co-cited journal in this field. The reference with citation bursts and trend topics showed that “ulcerative colitis,” “inflammatory bowel disease,” “microbiome,” “transcriptomics,” “genomics,” “metabolomics,” “proteomics,” “dysbiosis,” “biomarkers,” “loci,” and “therapy” are currently research hotspots.ConclusionOur study presents several important insights into the research trends and developments in the field of omics in UC, which will provide key information for further research.
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Affiliation(s)
- He Zhang
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Yuanyuan Ni
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hangyu Ji
- Office of Good Clinical Practice, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hongliang Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Shaoneng Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
- *Correspondence: Shaoneng Liu
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Donovan B, Spiel M. Inflammatory Bowel Disease in the Childbearing Adult and Newborn. Neoreviews 2023; 24:10-23. [PMID: 36587009 DOI: 10.1542/neo.24-1-e10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Inflammatory bowel disease (IBD) often affects people in their childbearing years and has implications for pregnancy outcomes, particularly as related to increased risk of preterm delivery and effects of immunosuppressive medications on the fetus. Ideally, people with IBD should attempt conception at a time when their disease is in remission to optimize pregnancy outcomes and reduce risks of flares. Generally, pregnant individuals should continue immunosuppressive medications throughout gestation in an attempt to control the disease. Maternal risks of IBD in pregnancy include exacerbated anemia, disease flare, cesarean delivery, and treatment risks. Fetal and neonatal risks include preterm birth, low birthweight, and medication exposures. There are too few clinical trials that include pregnant or breastfeeding patients to analyze the risk/benefit profile of immunosuppressive medications for IBD treatment during pregnancy, limiting the amount of data available to guide medical treatment in this population. More studies are needed on IBD therapies, particularly as more biologics are developed and become the mainstay of treatment. Neonatal clinicians should be aware of in utero medication exposure to help guide decisions regarding newborn care.
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Affiliation(s)
- Bridget Donovan
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA
| | - Melissa Spiel
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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Lichen Sclerosus: A Current Landscape of Autoimmune and Genetic Interplay. Diagnostics (Basel) 2022; 12:diagnostics12123070. [PMID: 36553077 PMCID: PMC9777366 DOI: 10.3390/diagnostics12123070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Lichen sclerosus (LS) is an acquired chronic inflammatory dermatosis predominantly affecting the anogenital area with recalcitrant itching and soreness. Progressive or persistent LS may cause urinary and sexual disturbances and an increased risk of local skin malignancy with a prevalence of up to 11%. Investigations on lipoid proteinosis, an autosomal recessive genodermatosis caused by loss-of-function mutations in the extracellular matrix protein 1 (ECM1) gene, led to the discovery of a humoral autoimmune response to the identical molecule in LS, providing evidence for an autoimmune and genetic counterpart targeting ECM1. This paper provides an overview of the fundamental importance and current issue of better understanding the immunopathology attributed to ECM1 in LS. Furthermore, we highlight the pleiotropic action of ECM1 in homeostatic and structural maintenance of skin biology as well as in a variety of human disorders possibly associated with impaired or gained ECM1 function, including the inflammatory bowel disease ulcerative colitis, Th2 cell-dependent airway allergies, T-cell and B-cell activation, and the demyelinating central nervous system disease multiple sclerosis, to facilitate sharing the concept as a plausible therapeutic target of this attractive molecule.
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Tuo S, Li C, Liu F, Zhu Y, Chen T, Feng Z, Liu H, Li A. A Novel Multitasking Ant Colony Optimization Method for Detecting Multiorder SNP Interactions. Interdiscip Sci 2022; 14:814-832. [PMID: 35788965 DOI: 10.1007/s12539-022-00530-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
MOTIVATION Linear or nonlinear interactions of multiple single-nucleotide polymorphisms (SNPs) play an important role in understanding the genetic basis of complex human diseases. However, combinatorial analytics in high-dimensional space makes it extremely challenging to detect multiorder SNP interactions. Most classic approaches can only perform one task (for detecting k-order SNP interactions) in each run. Since prior knowledge of a complex disease is usually not available, it is difficult to determine the value of k for detecting k-order SNP interactions. METHODS A novel multitasking ant colony optimization algorithm (named MTACO-DMSI) is proposed to detect multiorder SNP interactions, and it is divided into two stages: searching and testing. In the searching stage, multiple multiorder SNP interaction detection tasks (from 2nd-order to kth-order) are executed in parallel, and two subpopulations that separately adopt the Bayesian network-based K2-score and Jensen-Shannon divergence (JS-score) as evaluation criteria are generated for each task to improve the global search capability and the discrimination ability for various disease models. In the testing stage, the G test statistical test is adopted to further verify the authenticity of candidate solutions to reduce the error rate. RESULT Three multiorder simulated disease models with different interaction effects and three real age-related macular degeneration (AMD), rheumatoid arthritis (RA) and type 1 diabetes (T1D) datasets were used to investigate the performance of the proposed MTACO-DMSI. The experimental results show that the MTACO-DMSI has a faster search speed and higher discriminatory power for diverse simulation disease models than traditional single-task algorithms. The results on real AMD data and RA and T1D datasets indicate that MTACO-DMSI has the ability to detect multiorder SNP interactions at a genome-wide scale. Availability and implementation: https://github.com/shouhengtuo/MTACO-DMSI/.
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Affiliation(s)
- Shouheng Tuo
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China.
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China.
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China.
| | - Chao Li
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Fan Liu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - YanLing Zhu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - TianRui Chen
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - ZengYu Feng
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Haiyan Liu
- School of Computer Science and Technology, Xi'an University of Posts and Telecommunications, Xi'an, 710121, Shaanxi, China
- Shaanxi Key Laboratory of Network Data Analysis and Intelligent Processing, Xi'an, 710121, Shaanxi, China
- Xi'an Key Laboratory of Big Data and Intelligent Computing, Xi'an, 710121, Shaanxi, China
| | - Aimin Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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Nielsen MI, de Haan N, Kightlinger W, Ye Z, Dabelsteen S, Li M, Jewett MC, Bagdonaite I, Vakhrushev SY, Wandall HH. Global mapping of GalNAc-T isoform-specificities and O-glycosylation site-occupancy in a tissue-forming human cell line. Nat Commun 2022; 13:6257. [PMID: 36270990 PMCID: PMC9587226 DOI: 10.1038/s41467-022-33806-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/30/2022] [Indexed: 12/25/2022] Open
Abstract
Mucin-type-O-glycosylation on proteins is integrally involved in human health and disease and is coordinated by an enzyme family of 20 N-acetylgalactosaminyltransferases (GalNAc-Ts). Detailed knowledge on the biological effects of site-specific O-glycosylation is limited due to lack of information on specific glycosylation enzyme activities and O-glycosylation site-occupancies. Here we present a systematic analysis of the isoform-specific targets of all GalNAc-Ts expressed within a tissue-forming human skin cell line, and demonstrate biologically significant effects of O-glycan initiation on epithelial formation. We find over 300 unique glycosylation sites across a diverse set of proteins specifically regulated by one of the GalNAc-T isoforms, consistent with their impact on the tissue phenotypes. Notably, we discover a high variability in the O-glycosylation site-occupancy of 70 glycosylated regions of secreted proteins. These findings revisit the relevance of individual O-glycosylation sites in the proteome, and provide an approach to establish which sites drive biological functions.
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Affiliation(s)
- Mathias I. Nielsen
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Noortje de Haan
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Weston Kightlinger
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark ,grid.16753.360000 0001 2299 3507Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Zilu Ye
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sally Dabelsteen
- grid.5254.60000 0001 0674 042XDepartment of Oral Medicine and Pathology, School of Dentistry, University of Copenhagen, Copenhagen, Denmark
| | - Minyan Li
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael C. Jewett
- grid.16753.360000 0001 2299 3507Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208 USA
| | - Ieva Bagdonaite
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y. Vakhrushev
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H. Wandall
- grid.5254.60000 0001 0674 042XCopenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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12
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Associations between Extracellular Matrix Protein 1 Gene Polymorphism and Progression of Liver Disease. Genet Res (Camb) 2022; 2022:9304264. [PMID: 36299684 PMCID: PMC9586790 DOI: 10.1155/2022/9304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/21/2022] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background Our study aimed to investigate the relationship between extracellular matrix 1 (ECM1) gene polymorphism and progression of liver fibrosis in the Chinese population. Methods A total 656 patients with hepatitis B virus (HBV) infection and 298 healthy individuals of the Chinese Han population were recruited for a retrospective case-control study. Of the disease group, 104 cases had chronic hepatitis B (CHB), 266 had LC, and 286 had hepatocellular carcinoma (HCC). Subjects were frequency-matched according to age and gender. Polymorphisms of the ECM1 gene were examined using the MassARRAY SNP genotyping method. Results There were no associations between genotype and allele frequencies of ECM1 rs3737240 and rs13294 loci with the risk of CHB and CHB-related HCC. After adjustment for age, sex, smoking status, and drinking habits, the GT genotype was dramatically related to a reduced risk of chronic HBV infection in both non-HCC (OR = 0.68, 95% CI: 0.49-0.94) and total chronic HBV infection patients (OR = 0.75, 95% CI: 0.56-1.00). Haplotype analyses revealed twelve protective haplotypes against total chronic HBV infection and four against non-HCC chronic HBV infection. Conclusion ECM1 gene polymorphism in rs3834087 and rs3754217 loci is associated with a reduced risk of chronic HBV infection but not with liver fibrosis development and the occurrence of HCC.
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13
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Abstract
Increasing insights into the immunopathogenesis of inflammatory bowel diseases [IBD] have led to the advent of targeted therapies that inhibit crucial mediators of the inflammatory process, thereby widening our available therapeutic armamentarium. Anti-tumour necrosis factor [anti-TNF] agents are still a mainstay of our therapeutic endeavours and the introduction of corresponding biosimilars has further widened their use. Nevertheless, only a subgroup of treated patients benefit from the initiated treatment and there is secondary non-response in the course of therapy. Initiation of subsequent therapy often poses a challenge to the treating physician, as non-response to primary anti-TNF treatment generally characterizes a patient group that is more treatment-resistant, which may be due to the immunological impregnation by prior anti-TNF exposure. At present, there is currently no guidance for the most appropriate second-line therapy after anti-TNF failure. Here, we review the efficacy of secondary biological therapy in anti-TNF-treated patients. We focus on and assess available clinical trial data of the emerging substance class of IL-23p19 inhibitors, which have demonstrated remarkable efficacy not only in anti-TNF-naïve but also refractory patients. We present molecular mechanisms that drive IL-23-mediated resistance to ongoing anti-TNF therapy and discuss the dynamic fluidity of the mucosal cytokine network in the course of therapy that perpetuates the mucosal inflammatory reaction. Translation of these findings into clinical practice might finally lead to initiation of the most appropriate therapy at the right time of the individual disease course, which would have important implications for the patient's probability of response to treatment.
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Affiliation(s)
- Raja Atreya
- Corresponding author: Raja Atreya, Professor of Medicine, Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany. Tel: +49-9131-85-35000; Fax: +49-9131-85-35209;
| | - Markus F Neurath
- Medical Clinic 1, Department of Medicine, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen, Germany,Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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14
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Sewell GW, Kaser A. Interleukin-23 in the Pathogenesis of Inflammatory Bowel Disease and Implications for Therapeutic Intervention. J Crohns Colitis 2022; 16:ii3-ii19. [PMID: 35553667 PMCID: PMC9097674 DOI: 10.1093/ecco-jcc/jjac034] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The interleukin-23 [IL-23] cytokine, derived predominantly from macrophages and dendritic cells in response to microbial stimulation, has emerged as a critical promoter of chronic intestinal inflammation. Genome-wide association studies linking variants in IL23R to disease protection, bolstered by experimental evidence from colitis models, and the successful application of therapies against the IL-12/IL-23 shared p40 subunit in the treatment of inflammatory bowel disease [IBD] all provide compelling evidence of a crucial role for IL-23 in disease pathogenesis. Moreover, targeting the p19 subunit specific for IL-23 has shown considerable promise in recent phase 2 studies in IBD. The relative importance of the diverse immunological pathways downstream of IL-23 in propagating mucosal inflammation in the gut, however, remains contentious. Here we review current understanding of IL-23 biology and explore its pleiotropic effects on T cells, and innate lymphoid, myeloid and intestinal epithelial cells in the context of the pathogenesis of IBD. We furthermore discuss these pathways in the light of recent evidence from clinical trials and indicate emerging targets amenable to therapeutic intervention and translation into clinical practice.
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Affiliation(s)
- Gavin W Sewell
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK,Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, UK
| | - Arthur Kaser
- Corresponding author: Arthur Kaser, Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK. Tel: +44 1223 331130;
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15
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Munir A, Hu L. Synthesized Drug from Medicinal Plant phytochemicals Effectively Targets ECM1 Gene Mutations in Ulcerative Colitis. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804130050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
:
Ulcerative colitis (UC); an inflammatory bowel disease primarily affects the mucosa of
the colon. Depending on its mode of appearance, it can affect either the entire colon or even the distal
rectum. UC can manifest in both genders and every generation, but most generally appear in people
between the ages of 15 and 30. The extracellular matrix protein-1 (ECM1) gene is an important
candidate, mutations leading to tissue damage in patients with ECM1 single-nucleotide polymorphisms
are likely to intensify tissue damage caused by Metalloproteinase9 resulting in UC. In this
analysis, approval for the synthesis of Chemical Compound was obtained from the scientific committee
of the Department of Traditional Chinese Medicine, Qilu Hospital, China. Several derivatives
used as UC therapy were selected to build the pharmacophore model, using a ligand-based pharmacophore
modeling approach and virtual screenings were done for the identification of suitable drug
compounds. The selected compound was then synthesized in-vitro and validated using the molecular
docking technique. The synthesized compound fulfills all the characteristics of the non-toxic existence
of other drug-likeness laws. The specific interactive amino acids found in the docked complex
are arginine (ARG):47, lysine (LYS):54, phenylalanine (PHE):141, aspargine (ASN):51, serine
(SER):219, histadine (HIS):144, PHE:214, valine(VAL):220, tyrosine(TYR):145, and TYR:284. The
interaction of the synthesized compound with mutated TYR:284 of ECM1 confirmed the viability
and safety of a drug molecule as a medication in Ulcerative Colitis care. In the future, its validity can
be explored in the laboratory and this synthesized compound can be used as a medication target in
clinical studies against TYR:284 mutation in the ECM1 gene.
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Affiliation(s)
- Anum Munir
- Department of Biotechnology, Comsats University Islamabad, Abbottabad Campus, 22010, Abbottabad, Pakistan
| | - Lianhai Hu
- Department of Traditional Chinese Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, No.
107 Wenhuaxi Road, Jinan, Shandong Province, 250012, China
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16
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Noel DD, Marinella P, Mauro G, Tripodi SI, Pin A, Serena A, Matteo B, Giuseppe FM, Patrizia A, Stefano C, Tommasini A, Raffaele B. Genetic Variants Assessing Crohn's Disease Pattern in Pediatric Inflammatory Bowel Disease Patients by a Clinical Exome Survey. Bioinform Biol Insights 2021; 15:11779322211055285. [PMID: 35002226 PMCID: PMC8728778 DOI: 10.1177/11779322211055285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/02/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) are complex, multifactorial disorders that comprise Crohn's disease (CD) and ulcerative colitis (UC). Recent discoveries have brought much attention to the genetic predisposition of patients with IBD. Here we evaluate the interaction between IBD genetic risk factors susceptibility and CD occurrence in an IBD pediatric patient population, performing a clinical exome survey. METHODS From February 2018 to April 2019, we collected blood samples from 7 pediatric patients with IBD concerns from several collaborating health centers and/or hospitals. Blood samples were processed by extracting and sequencing DNA for a clinical exome survey. Shophia-DDM-v3-4 platform allowed sequenced reads alignment on hg19 genome as well as genetic variant calling. Both IBD risk and pathogenic genetic variants covered by at least 20 reads were selected for subjacent analysis. RESULTS Normality and Bartlett tests of both risk and pathogenic genetic variants suggested random and heterogeneous distribution of these variants in this group of IBD pediatric patients. P value clustering analysis by processing 157 IBD risk factors revealed genetic heterogeneity in IBD population and suggested two pathways influencing IBD development. In particular, (1) genetic variants associated with autoimmune and (2) metabolic diseases and CD risk factors (rs2066844 and rs2241880 single nucleotide polymorphism variants, respectively, of genes NOD2 and ATG16L) were identified in distinct clusters of IBD patients (P < .05). Moreover, the heterogeneous distribution of the following variants rs10065172 (IRGM), rs1805010 (IL4R), rs5030737 (MBL2), and rs33995883 (LRRK2) in this group of IBD patients was consistent with their random distribution in that population. CONCLUSION Our study revealed specific genetic variants linked to CD susceptibility, autoimmune and/or innate immunodeficiency as well as to metabolic defects, as favoring factors of IBD, suggesting the valuable role of next generation sequencing (NGS) approaches in IBD molecular diagnostic procedures.
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Affiliation(s)
- Dago Dougba Noel
- Department of Clinical and Experimental
Sciences, Institute of Molecular Medicine Angelo Nocivelli, University of Brescia
and Children’s Hospital, ASST Spedali Civili, Brescia, Italy
- Unit of Biostatistics and
Biomathematics & Unit of Bioinformatics, Department of Molecular and
Translational Medicine, University of Brescia, Brescia, Italy
- Department of Genetic and Biochemistry,
Genetic Research Unit, Peleforo Gon Coulibaly University of Korhogo, Korhogo, Ivory
Coast
| | - Pinelli Marinella
- Department of Clinical and Experimental
Sciences, Institute of Molecular Medicine Angelo Nocivelli, University of Brescia
and Children’s Hospital, ASST Spedali Civili, Brescia, Italy
| | - Giacomelli Mauro
- Department of Clinical and Experimental
Sciences, Institute of Molecular Medicine Angelo Nocivelli, University of Brescia
and Children’s Hospital, ASST Spedali Civili, Brescia, Italy
| | - Serena Ilaria Tripodi
- Department of Clinical and Experimental
Sciences, Institute of Molecular Medicine Angelo Nocivelli, University of Brescia
and Children’s Hospital, ASST Spedali Civili, Brescia, Italy
| | - Alessia Pin
- IRCCS Materno Infantile Burlo Garofolo,
Trieste, Italy
| | | | | | | | - Alvisi Patrizia
- Pediatric Gastroenterology Unit,
Maggiore Hospital, Bologna, Italy
| | - Calza Stefano
- Unit of Biostatistics and
Biomathematics & Unit of Bioinformatics, Department of Molecular and
Translational Medicine, University of Brescia, Brescia, Italy
| | | | - Badolato Raffaele
- Department of Clinical and Experimental
Sciences, Institute of Molecular Medicine Angelo Nocivelli, University of Brescia
and Children’s Hospital, ASST Spedali Civili, Brescia, Italy
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17
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Functional interrogation of autoimmune disease genetics using CRISPR/Cas9 technologies and massively parallel reporter assays. Semin Immunopathol 2021; 44:137-147. [PMID: 34508276 PMCID: PMC8837574 DOI: 10.1007/s00281-021-00887-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023]
Abstract
Genetic studies, including genome-wide association studies, have identified many common variants that are associated with autoimmune diseases. Strikingly, in addition to being frequently observed in healthy individuals, a number of these variants are shared across diseases with diverse clinical presentations. This highlights the potential for improved autoimmune disease understanding which could be achieved by characterising the mechanism by which variants lead to increased risk of disease. Of particular interest is the potential for identifying novel drug targets or of repositioning drugs currently used in other diseases. The majority of autoimmune disease variants do not alter coding regions and it is often difficult to generate a plausible hypothetical mechanism by which variants affect disease-relevant genes and pathways. Given the interest in this area, considerable effort has been invested in developing and applying appropriate methodologies. Two of the most important technologies in this space include both low- and high-throughput genomic perturbation using the CRISPR/Cas9 system and massively parallel reporter assays. In this review, we introduce the field of autoimmune disease functional genomics and use numerous examples to demonstrate the recent and potential future impact of these technologies.
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18
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Moreira TG, Mangani D, Cox LM, Leibowitz J, Lobo ELC, Oliveira MA, Gauthier CD, Nakagaki BN, Willocq V, Song A, Guo L, Lima DCA, Murugaiyan G, Butovsky O, Gabriely G, Anderson AC, Rezende RM, Faria AMC, Weiner HL. PD-L1 + and XCR1 + dendritic cells are region-specific regulators of gut homeostasis. Nat Commun 2021; 12:4907. [PMID: 34389726 PMCID: PMC8363668 DOI: 10.1038/s41467-021-25115-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal mucosa constitutes an environment of closely regulated immune cells. Dendritic cells (DC) interact with the gut microbiome and antigens and are important in maintaining gut homeostasis. Here, we investigate DC transcriptome, phenotype and function in five anatomical locations of the gut lamina propria (LP) which constitute different antigenic environments. We show that DC from distinct gut LP compartments induce distinct T cell differentiation and cytokine secretion. We also find that PD-L1+ DC in the duodenal LP and XCR1+ DC in the colonic LP comprise distinct tolerogenic DC subsets that are crucial for gut homeostasis. Mice lacking PD-L1+ and XCR1+ DC have a proinflammatory gut milieu associated with an increase in Th1/Th17 cells and a decrease in Treg cells and have exacerbated disease in the models of 5-FU-induced mucositis and DSS-induced colitis. Our findings identify PD-L1+ and XCR1+ DC as region-specific physiologic regulators of intestinal homeostasis.
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Affiliation(s)
- Thais G Moreira
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura M Cox
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Leibowitz
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eduardo L C Lobo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariana A Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Christian D Gauthier
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda N Nakagaki
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valerie Willocq
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anya Song
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lydia Guo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David C A Lima
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gopal Murugaiyan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Oleg Butovsky
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Galina Gabriely
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rafael M Rezende
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana Maria C Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Howard L Weiner
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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19
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Attauabi M, Zhao M, Bendtsen F, Burisch J. Systematic review and meta-analysis: the impact of co-occurring immune-mediated inflammatory diseases on the disease localization and behavior of Crohn's disease. Therap Adv Gastroenterol 2021; 14:17562848211004839. [PMID: 34234844 PMCID: PMC8226240 DOI: 10.1177/17562848211004839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Patients with Crohn's disease (CD) are at increased risk of co-occurring immune-mediated inflammatory diseases (IMIDs). As discrepancy exists regarding the phenotypic presentation of CD among patients with such co-occurring IMIDs, we aimed to conduct a systematic review with meta-analysis characterizing the phenotype of CD among this subgroup of patients. METHODS PubMed, Embase, and Scopus were searched from their earliest records to October 2019 for studies reporting the behavior and localization of CD according to the Vienna or Montreal Classifications and CD-related surgery in patients with co-occurring IMIDs. These studies were the subject of a random effect meta-analysis. RESULTS After reviewing 24,413 studies, we identified a total of 23 studies comprising 1572 and 35,043 CD patients with and without co-occurring IMIDs, respectively, that fulfilled our inclusion criteria. Overall, patients with co-occurring IMIDs were more likely to have upper gastrointestinal inflammation than were patients without co-occurring IMIDs [relative risk (RR) = 1.49 (95% confidence interval (CI) 1.09-2.04), p = 0.01, I 2 = 7%]. In addition, presence of primary sclerosing cholangitis (PSC) was associated with a lower occurrence of ileal affection [RR = 0.44 (95% CI 0.24-0.81), p < 0.01, I 2 = 32%], increased occurrence of colonic affection [RR = 1.78 (95% CI 1.33-2.38), p < 0.01, I 2 = 32%] and an increased likelihood of non-stricturing and non-penetrating behavior [RR = 1.43 (95% CI 0.97-2.11), p = 0.07, I 2 = 86%]. The latter reached significance when cumulating different IMIDs [RR = 1.30 (95% CI 1.09-1.55), p < 0.01, I 2 = 88%]. CD patients with PSC also underwent fewer CD-related surgeries [RR = 0.55 (95% CI 0.34-0.88), p = 0.01, I 2 = 0%], irrespective of CD location or behavior. CONCLUSION This study emphasizes that CD patients with co-existing PSC are likely to have a unique inflammatory distribution primarily confined to the colon, while patients with IMIDs in general have higher likelihood of affection of upper gastrointestinal tract and a non-stricturing and non-penetrating behavior. As such a phenotype of CD is typically associated with a milder disease course; future studies are needed to confirm these results.
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Affiliation(s)
- Mohamed Attauabi
- Gastrounit, Medical Section, Copenhagen
University Hospital Hvidovre, Kettegaard Alle 30, Denmark
- Copenhagen Center for Inflammatory Bowel
Disease in Children, Adolescents and Adults, University of Copenhagen,
Hvidovre Hospital, Denmark
| | - Mirabella Zhao
- Gastrounit, Medical Section, Copenhagen
University Hospital, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel
Disease in Children, Adolescents and Adults, University of Copenhagen,
Hvidovre Hospital, Denmark
| | - Flemming Bendtsen
- Gastrounit, Medical Section, Copenhagen
University Hospital, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel
Disease in Children, Adolescents and Adults, University of Copenhagen,
Hvidovre Hospital, Denmark
| | - Johan Burisch
- Gastrounit, Medical Section, Copenhagen
University Hospital, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel
Disease in Children, Adolescents and Adults, University of Copenhagen,
Hvidovre Hospital, Denmark
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20
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Wu PB, Zhang Y, Nie G, Huang X, Yu YJ, Yin AN, Zhou R, He CP, Wang P. Association between genetic variants in ZNF365 and inflammatory bowel disease risk in Caucasians: a meta-analysis and trial sequential analysis. Expert Rev Clin Immunol 2021; 17:915-921. [PMID: 34092165 DOI: 10.1080/1744666x.2021.1939012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE The published studies regarding the relationships between zinc finger 365 (ZNF365) polymorphisms and inflammatory bowel disease (IBD) risk in Caucasians have yielded conflicting results. Therefore, we performed a meta-analysis to clarify this issue. METHODS The Electronic databases of PubMed, Web of Science, Wiley Online Library, and EMBASE were searched for eligible studies up to 31 November 2020. The quality of eligible studies was evaluated using the Newcastle-Ottawa Scale. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) under different genetic models were calculated to assess the strength of associations. RESULTS A total of 22 relevant case-control studies with 9542 ulcerative colitis (UC) patients and 13,886 controls, as well as 13,651 Crohn's disease (CD) patients and 15,256 controls, were involved in our meta-analysis. rs10761659 polymorphism significantly decreased CD and UC risk (except for the heterozygous model and the dominant model in UC), and rs10995271 polymorphism was significantly associated with UC (except for the heterozygous model and dominant model) rather than CD. CONCLUSIONS The meta-analysis demonstrated that the rs10761659 polymorphism might be a protective factor for both UC and CD in Caucasians, while the rs10995271 polymorphism might be a risk factor for UC rather than CD in Caucasians.
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Affiliation(s)
- Peng-Bo Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yu Zhang
- Infrastructure Management Department, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Gang Nie
- Department of Dermatovenereology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong China
| | - Xu Huang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Yuan-Jie Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - An-Ning Yin
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Rui Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Chun-Ping He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei China
| | - Peng Wang
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan Hubei Province, China
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Wang J, Liu H, Wang Y, Wu J, Wang C, Liu K, Qin Q. The Polymorphisms of Interleukin-12B Gene and Susceptibility to Inflammatory Bowel Diseases: A Meta-analysis and Trial Sequential Analysis. Immunol Invest 2021; 50:987-1006. [PMID: 33390082 DOI: 10.1080/08820139.2020.1863981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Objective: Inflammatory bowel disease (IBD) is a heterogeneous complex disease referring to two chronic disorders: Crohn's disease (CD) and ulcerative colitis (UC). To clarify the relationship between IL-12B gene polymorphisms and susceptibility to CD and UC, a meta-analysis was conducted.Methods: A comprehensive search of the PubMed, Web of Science, Embase and Cochrane databases was conducted up to Oct 2019. Studies evaluating the relationship between risk of IBD and variants of IL-12B (rs6887695, rs3212227 and rs10045431) were included. Odds ratio (OR) and 95% confidence interval (CI) were calculated. Trial sequential analysis (TSA) was implemented to estimate the required information size (RIS) and evaluate the credibility of the meta-analysis results.Results: Seventeen studies containing 9827 patients with CD, 7583 patients with UC and 16044 controls were included. The results showed significant association between rs6887695 polymorphism and susceptibility to CD (allele model: OR = 1.17, 95% CI: 1.12-1.22) and UC (allele model: OR = 1.16, 95% CI: 1.09-1.23), and "C" allele carriers had a higher risk, with TSA conclusive. For rs10045431, no significant association with CD susceptibility was identified, while a significantly increased risk in UC was found (allele mode: OR = 1.16, 95% CI: 1.07-1.25), both results were conclusive according to TSA. No significant association between rs3212227 and CD or UC susceptibility was found, and TSA research warranted further investigation to certify the results. No significant heterogeneity was found.Conclusion: IL-12B rs6887695 polymorphism was associated with increased risk of CD and UC, while IL-12B rs10045431 polymorphism might only be correlated with the risk of UC.Abbreviations: IBD: inflammatory bowel disease; CD: Crohn's disease; UC: ulcerative colitis; IL-12B: interleukin-12B; OR: odds ratio; CI: confidence interval; TSA: trial sequential analysis; RIS: required information size; DCs: dendritic cells; NK: nature killer; APCs: antigen-presenting cells; TNF: tumor necrosis factor; SNP: single nucleotide polymorphisms; HWE: Hardy-Weinberg equilibrium; NOS: Newcastle-Ottawa scale; RRR: relative risk reduction.
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Affiliation(s)
- Jing Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hong Liu
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yadan Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Jing Wu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Canghai Wang
- Department of Gastroenterology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Kuiliang Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Qin Qin
- Department of Prevention and Health Care, Zhongshan Hospital, Xiamen University, Xiamen, China
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Ding J, Frantzeskos A, Orozco G. Functional genomics in autoimmune diseases. Hum Mol Genet 2020; 29:R59-R65. [PMID: 32420598 PMCID: PMC7530520 DOI: 10.1093/hmg/ddaa097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Associations between genetic loci and increased susceptibility to autoimmune disease have been well characterized, however, translating this knowledge into mechanistic insight and patient benefit remains a challenge. While improvements in the precision, completeness and accuracy of our genetic understanding of autoimmune diseases will undoubtedly be helpful, meeting this challenge will require two interlinked problems to be addressed: first which of the highly correlated variants at an individual locus is responsible for increased disease risk, and second what are the downstream effects of this variant. Given that the majority of loci are thought to affect non-coding regulatory elements, the second question is often reframed as what are the target gene(s) and pathways affected by causal variants. Currently, these questions are being addressed using a wide variety of novel techniques and datasets. In many cases, these approaches are complementary and it is likely that the most accurate picture will be generated by consolidating information relating to transcription, regulatory activity, chromatin accessibility, chromatin conformation and readouts from functional experiments, such as genome editing and reporter assays. It is clear that it will be necessary to gather this information from disease relevant cell types and conditions and that by doing so our understanding of disease etiology will be improved. This review is focused on the field of autoimmune disease functional genomics with a particular focus on the most exciting and significant research to be published within the last couple of years.
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Affiliation(s)
- James Ding
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Antonios Frantzeskos
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
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Wu PB, Wu XM, Qian R, Hong C, Yitian G, Zhang G, Yu YJ. Association between IL12B polymorphisms and inflammatory bowel disease in Caucasian population: A meta-analysis. Cytokine 2020; 136:155296. [PMID: 32947150 DOI: 10.1016/j.cyto.2020.155296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Published studies on association between IL12B (G/A) rs10045431, (T/C)rs6887695 polymorphisms and inflammatory bowel disease (IBD) risk in Caucasian population have yielded conflicting results. The aim of this study was to potentially provide more reliable conclusions by conducting a meta-analysis. METHODS Published studies concerned association between IL12B rs10045431, rs6887695 polymorphisms and IBD were searched from the Wiley Online Library, PubMed, Web of Science and the CNKI database. The odds ratio (OR) with 95% confidence interval (CI) was calculated to evaluate the strength of the relationship. The false positive report probabilities (FPRPs) test and trial sequential analysis (TSA) was performed to investigated the reliability of results. RESULTS A total of 20 studies comprising 10761 Crohn's disease (CD), 10921 ulcerative colitis (UC) and 18381 controls were included in this meta-analysis. Overall, the pooled results showed that IL12B rs6887695 polymorphism significantly increased both CD and UC risk under all model, while IL12B rs10045431 polymorphism dramatically decreased both CD and UC risk under all model. FPRP and TSA demonstrated that above associations was confirmed in the present study. CONCLUSION The results of meta-analysis indicate IL12B rs10045431 and rs6887695 polymorphisms significantly associate with IBD in Caucasian population.
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Affiliation(s)
- Peng-Bo Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China
| | - Xiao-Man Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China
| | - Rao Qian
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China
| | - Chai Hong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China
| | - Guo Yitian
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China
| | - Guo Zhang
- Department of Gastroenterology, The People's Hospital of Guangxi Zhuang Autonomous Region, 35 Taoyuan Road, Nanning, China
| | - Yuan-Jie Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuhan, China.
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Ameliorated Autoimmune Arthritis and Impaired B Cell Receptor-Mediated Ca 2+ Influx in Nkx2-3 Knock-out Mice. Int J Mol Sci 2020; 21:ijms21176162. [PMID: 32859051 PMCID: PMC7503974 DOI: 10.3390/ijms21176162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
B cells play a crucial role in the pathogenesis of rheumatoid arthritis. In Nkx2-3-deficient mice (Nkx2-3−/−) the spleen’s histological structure is fundamentally changed; therefore, B cell homeostasis is seriously disturbed. Based on this, we were curious, whether autoimmune arthritis could be induced in Nkx2-3−/− mice and how B cell activation and function were affected. We induced arthritis with immunization of recombinant human proteoglycan aggrecan G1 domain in Nkx2-3−/− and control BALB/c mice. We followed the clinical picture, characterized the radiological changes, the immune response, and intracellular Ca2+ signaling of B cells. Incidence of the autoimmune arthritis was lower, and the disease severity was milder in Nkx2-3−/− mice than in control BALB/c mice. The radiological changes were in line with the clinical picture. In Nkx2-3−/− mice, we measured decreased antigen-induced proliferation and cytokine production in spleen cell cultures; in the sera, we found less anti-CCP-IgG2a, IL-17 and IFNγ, but more IL-1β, IL-4 and IL-6. B cells isolated from the lymph nodes of Nkx2-3−/− mice showed decreased intracellular Ca2+ signaling compared to those isolated from BALB/c mice. Our findings show that the transcription factor Nkx2-3 might regulate the development of autoimmune arthritis most likely through modifying B cell activation.
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Tang L, Xu M. Candidate polymorphisms and susceptibility to inflammatory bowel disease: A systematic review and meta-analysis. Gene X 2020; 753:144814. [DOI: 10.1016/j.gene.2020.144814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022] Open
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Kim TO, Park DI, Han YK, Kang K, Park SG, Park HR, Yi JM. Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad ( FHIT) Gene as a New Promising Biomarker of Crohn's Disease. J Clin Med 2020; 9:jcm9051338. [PMID: 32375395 PMCID: PMC7291297 DOI: 10.3390/jcm9051338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel disease is known to be associated with a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interactions with environmental factors, particularly epigenetic factors, can also significantly contribute to the development of inflammatory bowel disease (IBD). Although many genome-wide association studies have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease, the role of epigenetic alterations based on molecular complications arising from Crohn’s disease (CD) is poorly understood. We employed an unbiased approach to define DNA methylation alterations in colonoscopy samples from patients with CD using the HumanMethylation450K BeadChip platform. Technical and functional validation was performed by methylation-specific PCR (MSP) and bisulfite sequencing of a validation set of 207 patients with CD samples. Immunohistochemistry (IHC) analysis was performed in the representative sample sets. DNA methylation profile in CD revealed that 135 probes (24 hypermethylated and 111 hypomethylated probes) were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in patients with CD compared with normal controls. We uniquely identified that the fragile histidine triad (FHIT) gene was hypermethylated in a disease-specific manner and its protein level was downregulated in patients with CD. Pathway analysis of the hypermethylated candidates further suggested putative molecular interactions relevant to IBD pathology. Our data provide information on the biological and clinical implications of DNA hypermethylated genes in CD, identifying FHIT methylation as a promising new biomarker for CD. Further study of the role of FHIT in IBD pathogenesis may lead to the development of new therapeutic targets.
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Affiliation(s)
- Tae-Oh Kim
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan 48108, Korea;
| | - Dong-Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
| | - Sae-Gwang Park
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, Gyeongsangnam do 50612, Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
- Correspondence: ; Tel.: +82-51-890-6734
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Kaur A, Goggolidou P. Ulcerative colitis: understanding its cellular pathology could provide insights into novel therapies. JOURNAL OF INFLAMMATION-LONDON 2020; 17:15. [PMID: 32336953 PMCID: PMC7175540 DOI: 10.1186/s12950-020-00246-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 04/07/2020] [Indexed: 12/16/2022]
Abstract
Dynamic interactions between the gastrointestinal epithelium and the mucosal immune system normally contribute to ensuring intestinal homeostasis and optimal immunosurveillance, but destabilisation of these interactions in genetically predisposed individuals can lead to the development of chronic inflammatory diseases. Ulcerative colitis is one of the main types of inflammatory diseases that affect the bowel, but its pathogenesis has yet to be completely defined. Several genetic factors and other inflammation-related genes are implicated in mediating the inflammation and development of the disease. Some susceptibility loci associated with increased risk of ulcerative colitis are found to be implicated in mucosal barrier function. Different biomarkers that cause damage to the colonic mucosa can be detected in patients, including perinuclear ANCA, which is also useful in distinguishing ulcerative colitis from other colitides. The choice of treatment for ulcerative colitis depends on disease severity. Therapeutic strategies include anti-tumour necrosis factor alpha (TNF-α) monoclonal antibodies used to block the production of TNF-α that mediates intestinal tract inflammation, an anti-adhesion drug that prevents lymphocyte infiltration from the blood into the inflamed gut, inhibitors of JAK1 and JAK3 that suppress the innate immune cell signalling and interferons α/β which stimulate the production of anti-inflammatory cytokines, as well as faecal microbiota transplantation. Although further research is still required to fully dissect the pathophysiology of ulcerative colitis, understanding its cellular pathology and molecular mechanisms has already proven beneficial and it has got the potential to identify further novel, effective targets for therapy and reduce the burden of this chronic disease.
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Affiliation(s)
- Amandip Kaur
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY UK
| | - Paraskevi Goggolidou
- Department of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton, WV1 1LY UK
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ECM1 is an essential factor for the determination of M1 macrophage polarization in IBD in response to LPS stimulation. Proc Natl Acad Sci U S A 2020; 117:3083-3092. [PMID: 31980528 DOI: 10.1073/pnas.1912774117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) comprises chronic relapsing disorders of the gastrointestinal tract characterized pathologically by intestinal inflammation and epithelial injury. Here, we uncover a function of extracellular matrix protein 1 (ECM1) in promoting the pathogenesis of human and mouse IBD. ECM1 was highly expressed in macrophages, particularly tissue-infiltrated macrophages under inflammatory conditions, and ECM1 expression was significantly induced during IBD progression. The macrophage-specific knockout of ECM1 resulted in increased arginase 1 (ARG1) expression and impaired polarization into the M1 macrophage phenotype after lipopolysaccharide (LPS) treatment. A mechanistic study showed that ECM1 can regulate M1 macrophage polarization through the granulocyte-macrophage colony-stimulating factor/STAT5 signaling pathway. Pathological changes in mice with dextran sodium sulfate-induced IBD were alleviated by the specific knockout of the ECM1 gene in macrophages. Taken together, our findings show that ECM1 has an important function in promoting M1 macrophage polarization, which is critical for controlling inflammation and tissue repair in the intestine.
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Tsianos VE, Kostoulas C, Gazouli M, Frillingos S, Georgiou I, Christodoulou DK, Katsanos KH, Tsianos EV. ATG16L1 T300A polymorphism is associated with Crohn's disease in a Northwest Greek cohort, but ECM1 T130M and G290S polymorphisms are not associated with ulcerative colitis. Ann Gastroenterol 2019; 33:38-44. [PMID: 31892796 PMCID: PMC6928472 DOI: 10.20524/aog.2019.0434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023] Open
Abstract
Background: Crohn’s disease (CD) and ulcerative colitis (UC) are well-described disease entities with unknown etiopathogenesis. Environmental, genetic, gut microbiota, and host immune response correlations have been implicated. The role of susceptibility gene polymorphisms, such as ATG16L1 T300A and ECM1 T130M and G290S, is well-described, although controversial findings have been reported. Methods: Two hundred five patients with inflammatory bowel disease (108 CD and 97 UC), and 223 healthy blood donors (control group) from the Northwest Greece region were genotyped for rs2241880 (T300A), rs3737240 (T130M) and rs13294 (G290S) single nucleotide polymorphisms. Genotyping was performed using the real-time polymerase chain reaction method. Results: The frequency of G allele was significantly higher in CD patients compared to the control group (P=0.029; odds ratio [OR] 1.45, 95% confidence interval [CI] 1.04-2.03). Carriers of two G alleles (T300A), compared to those carrying only one, were 1.3 times more susceptible to CD (P=0.022; OR 2.45, 95%CI 1.14-5.27). In CD patients, the presence of the T300A polymorphism indicates a possible protective effect against developing a penetrating (B3) phenotype, while in UC patients, presence of the T300A polymorphism, indicates a possible protective effect against developing joint-involving extraintestinal manifestations. Conclusion: Our study found a significant association of the T300A polymorphism with CD susceptibility, suggesting that CD occurrence in our population has a strong genetic background, with the T300A G allele having an additive effect.
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Affiliation(s)
- Vasileios E Tsianos
- Research Laboratory of Immunology, Faculty of Medicine, School of Health Sciences, University of Ioannina (Vasileios E. Tsianos)
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina (Charilaos Kostoulas, Ioannis Georgiou)
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens (Maria Gazouli)
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina (Stathis Frillingos)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina (Charilaos Kostoulas, Ioannis Georgiou)
| | - Dimitrios K Christodoulou
- Department of Gastroenterology, University Hospital of Ioannina, Faculty of Medicine, School of Health Sciences, University of Ioannina (Dimitrios K. Christodoulou, Konstantinos H. Katsanos)
| | - Konstantinos H Katsanos
- Department of Gastroenterology, University Hospital of Ioannina, Faculty of Medicine, School of Health Sciences, University of Ioannina (Dimitrios K. Christodoulou, Konstantinos H. Katsanos)
| | - Epameinondas V Tsianos
- Faculty of Medicine, School of Health Sciences, University of Ioannina (Epameinondas V. Tsianos), Greece
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Parkes M. IBD BioResource: an open-access platform of 25 000 patients to accelerate research in Crohn's and Colitis. Gut 2019; 68:1537-1540. [PMID: 31270165 PMCID: PMC6709775 DOI: 10.1136/gutjnl-2019-318835] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 12/19/2022]
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Chandra N, Srivastava A, Kumar S. Bacterial biofilms in human gastrointestinal tract: An intricate balance between health and inflammatory bowel diseases. World J Pharmacol 2019; 8:26-40. [DOI: 10.5497/wjp.v8.i3.26] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) has been a worldwide health problem. It is characterized by severe intestinal inflammation due to immune responses against the gut microbes in genetically susceptible individuals. The understanding of gut microbiota for its composition and complex interaction in normal and diseased conditions has been assisted by the use of molecular, metagenomics and meta transcriptomics studies. The alteration of intestinal microbiota is the key determinant in the degree of inflammation caused and the prolonged course of disease. The relationship between luminal gut bacteria and innate immunity is also of prime significance. Such developments have further led to the search of specific (including bacteria and fungi) as a causative agent of IBD. Although detailed research has been done for the role of gut microbiota in IBD, molecular mechanisms and related gene expression are still not well understood in this disease, which hampers the generation of effective therapeutic agents for IBD. This paper assessed various factors contributing to IBD, genetic dysbiosis and pathogenic influence in the gut microbiota, interactions such as microbiome-host immune system interaction and microbe-microbe interactions involved in IBD, currently available IBD therapies, followed by a detailed review on bacterial infections that might be involved in IBD, globally and specifically in India.
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Affiliation(s)
- Niharika Chandra
- Faculty of Biotechnology, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Ankita Srivastava
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Sunil Kumar
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
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Khan I, Ullah N, Zha L, Bai Y, Khan A, Zhao T, Che T, Zhang C. Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome. Pathogens 2019; 8:pathogens8030126. [PMID: 31412603 PMCID: PMC6789542 DOI: 10.3390/pathogens8030126] [Citation(s) in RCA: 389] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic complex inflammatory gut pathological condition, examples of which include Crohn’s disease (CD) and ulcerative colitis (UC), which is associated with significant morbidity. Although the etiology of IBD is unknown, gut microbiota alteration (dysbiosis) is considered a novel factor involved in the pathogenesis of IBD. The gut microbiota acts as a metabolic organ and contributes to human health by performing various physiological functions; deviation in the gut flora composition is involved in various disease pathologies, including IBD. This review aims to summarize the current knowledge of gut microbiota alteration in IBD and how this contributes to intestinal inflammation, as well as explore the potential role of gut microbiota-based treatment approaches for the prevention and treatment of IBD. The current literature has clearly demonstrated a perturbation of the gut microbiota in IBD patients and mice colitis models, but a clear causal link of cause and effect has not yet been presented. In addition, gut microbiota-based therapeutic approaches have also shown good evidence of their effects in the amelioration of colitis in animal models (mice) and IBD patients, which indicates that gut flora might be a new promising therapeutic target for the treatment of IBD. However, insufficient data and confusing results from previous studies have led to a failure to define a core microbiome associated with IBD and the hidden mechanism of pathogenesis, which suggests that well-designed randomized control trials and mouse models are required for further research. In addition, a better understanding of this ecosystem will also determine the role of prebiotics and probiotics as therapeutic agents in the management of IBD.
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Affiliation(s)
- Israr Khan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Naeem Ullah
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Lajia Zha
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Yanrui Bai
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Ashiq Khan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Probiotics and Biological Feed Research Center, Lanzhou University, Lanzhou 730000, China
| | - Tang Zhao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China
| | - Tuanjie Che
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou 730000, China
| | - Chunjiang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, China.
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou 730000, China.
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou 730000, China.
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Pharmacological effects of TAK-828F: an orally available RORγt inverse agonist, in mouse colitis model and human blood cells of inflammatory bowel disease. Inflamm Res 2019; 68:493-509. [DOI: 10.1007/s00011-019-01234-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
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Vojkovics D, Kellermayer Z, Gábris F, Schippers A, Wagner N, Berta G, Farkas K, Balogh P. Differential Effects of the Absence of Nkx2-3 and MAdCAM-1 on the Distribution of Intestinal Type 3 Innate Lymphoid Cells and Postnatal SILT Formation in Mice. Front Immunol 2019; 10:366. [PMID: 30891037 PMCID: PMC6413488 DOI: 10.3389/fimmu.2019.00366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/13/2019] [Indexed: 01/08/2023] Open
Abstract
Seeding of leukocytes to developing lymphoid tissues in embryonic and early postnatal age and to the mucosa throughout adulthood depends on the interaction between endothelial MAdCAM-1 addressin and its cognate ligand α4β7 integrin. Nkx2-3 as a transcriptional regulator of MAdCAM-1 controls vascular patterning in visceral lymphoid tissues in mice, and has been identified as a susceptibility factor for inflammatory bowel diseases in humans, associated with lymphoid neogenesis in the inflamed intestines. The role of Nkx2-3 in the organogenesis of the solitary intestinal lymphoid tissues (SILTs) involving type 3 innate lymphoid cells (ILC3) is still unknown. Here we investigated the effect of Nkx2-3 on the postnatal distribution of intestinal ILC3s and the development of SILTs, comparing these to mice lacking MAdCAM-1, but preserving Nkx2-3. At 1 week of age small intestines (SI) contained significantly higher number of ILC3s relative to the colon, with a substantial reduction in MAdCAM-1−/− mice compared to C57BL/6 controls. One week later SI ILC3 number decreased in all genotypes, the number of colonic ILC3 of both Nkx2-3-deficient and Nkx2-3-heterozygous mice significantly increased. On the fourth postnatal week a further reduction of SI ILC3s was observed in both Nkx2-3-deficient and Nkx2-3-heterozygous mice, while in the colon the number of ILC3s showed a significant reduction in all genotypes. At 1 week of age only sporadic SILT components were present in all genotypes. By the second week mice deficient for either Nkx2-3 or MAdCAM-1 showed absence of SILT maturation compared to their relevant controls, lacking mature isolated lymphoid follicles (ILF). By the fourth week both Nkx2-3-deficient and Nkx2-3-heterozygous mice showed a similar distribution of ILFs relative to cryptopatches (CP), whereas in MAdCAM-1−/− mice CPs and immature ILFs were present, mature ILFs were scarce. Our data demonstrate that the complete absence of MAdCAM-1 partially impairs intestinal seeding of ILC3s and causes partial blockade of SILT maturation, without affecting peripheral lymph node development. In contrast, the inactivation of Nkx2-3 permits postnatal seeding, and its blocking effect on SILT maturation prevails at later stage, thus other adhesion molecules may compensate for the intestinal homing of ILC3s in the absence of MAdCAM-1.
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Affiliation(s)
- Dóra Vojkovics
- Department of Immunology and Biotechnology, Clinical Center, University of Pécs, Pécs, Hungary.,Lymphoid Organogenesis Research Group, Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Zoltán Kellermayer
- Department of Immunology and Biotechnology, Clinical Center, University of Pécs, Pécs, Hungary.,Lymphoid Organogenesis Research Group, Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Fanni Gábris
- Department of Immunology and Biotechnology, Clinical Center, University of Pécs, Pécs, Hungary.,Lymphoid Organogenesis Research Group, Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Angela Schippers
- Department of Pediatrics, University Hospital RWTH, Aachen, Germany
| | - Norbert Wagner
- Department of Pediatrics, University Hospital RWTH, Aachen, Germany
| | - Gergely Berta
- Central Electron Microscope Laboratory, Department of Medical Biology, Medical School, University of Pécs, Pécs, Hungary
| | - Kornélia Farkas
- Department of Bioanalytics, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Balogh
- Department of Immunology and Biotechnology, Clinical Center, University of Pécs, Pécs, Hungary.,Lymphoid Organogenesis Research Group, Szentágothai Research Center, University of Pécs, Pécs, Hungary
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Kellermayer Z, Vojkovics D, Dakah TA, Bodó K, Botz B, Helyes Z, Berta G, Kajtár B, Schippers A, Wagner N, Scotto L, O'Connor OA, Arnold HH, Balogh P. IL-22-Independent Protection from Colitis in the Absence of Nkx2.3 Transcription Factor in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1833-1844. [PMID: 30700585 DOI: 10.4049/jimmunol.1801117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/31/2018] [Indexed: 01/03/2023]
Abstract
The transcription factor Nkx2.3 regulates the vascular specification of Peyer patches in mice through determining endothelial addressin preference and may function as a susceptibility factor in inflammatory bowel diseases in humans. We wished to analyze the role of Nkx2.3 in colonic solitary intestinal lymphoid tissue composition and in colitis pathogenesis. We studied the colonic solitary intestinal lymphoid tissue of Nkx2.3-deficient mice with immunofluorescence and flow cytometry. Colitis was induced in mice using 2.5% dextran sodium sulfate, and severity was assessed with histology, flow cytometry, and quantitative PCR. We found that the lack of Nkx2.3 impairs maturation of isolated lymphoid follicles and attenuates dextran sodium sulfate-induced colitis independent of endothelial absence of mucosal addressin cell-adhesion molecule-1 (MAdCAM-1), which was also coupled with enhanced colonic epithelial regeneration. Although we observed increased numbers of group 3 innate lymphoid cells and Th17 cells and enhanced transcription of IL-22, Ab-mediated neutralization of IL-22 did not abolish the protection from colitis in Nkx2.3-deficient mice. Nkx2.3-/- hematopoietic cells could not rescue wild-type mice from colitis. Using LacZ-Nkx2.3 reporter mice, we found that Nkx2.3 expression was restricted to VAP-1+ myofibroblast-like pericryptal cells. These results hint at a previously unknown stromal role of Nkx2.3 as driver of colitis and indicate that Nkx2.3+ stromal cells play a role in epithelial cell homeostasis.
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Affiliation(s)
- Zoltán Kellermayer
- Department of Immunology and Biotechnology, Clinical Center, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
- Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Dóra Vojkovics
- Department of Immunology and Biotechnology, Clinical Center, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
- Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Tareq Abu Dakah
- Department of Immunology and Biotechnology, Clinical Center, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Kornélia Bodó
- Department of Immunology and Biotechnology, Clinical Center, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
| | - Bálint Botz
- Molecular Pharmacology Research Group, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
- Department of Radiology, Clinical Center, University of Pécs, Pécs H-7624, Hungary
| | - Zsuzsanna Helyes
- Molecular Pharmacology Research Group, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs H-7624, Hungary
| | - Gergely Berta
- Department of Medical Biology and Central Electron Microscope Laboratory, Medical School, University of Pécs, Pécs H-7624, Hungary
| | - Béla Kajtár
- Department of Pathology, Clinical Center, University of Pécs, Pécs H-7624, Hungary
| | - Angela Schippers
- Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen 52074, Germany
| | - Norbert Wagner
- Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen 52074, Germany
| | - Luigi Scotto
- Department of Experimental Therapeutics, Columbia University Medical Center, New York 10019, NY
| | - Owen A O'Connor
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York 10019, NY; and
| | - Hans-Henning Arnold
- Department of Cell and Molecular Biology, Institute of Biochemistry and Biotechnology, Technical University of Braunschweig, Braunschweig 38106, Germany
| | - Péter Balogh
- Department of Immunology and Biotechnology, Clinical Center, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary;
- Lymphoid Organogenesis Research Group, Szentágothai János Research Center, University of Pécs, Pécs H-7624, Hungary
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Roles of Autophagy-Related Genes in the Pathogenesis of Inflammatory Bowel Disease. Cells 2019; 8:cells8010077. [PMID: 30669622 PMCID: PMC6356351 DOI: 10.3390/cells8010077] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 12/13/2022] Open
Abstract
Autophagy is an intracellular catabolic process that is essential for a variety of cellular responses. Due to its role in the maintenance of biological homeostasis in conditions of stress, dysregulation or disruption of autophagy may be linked to human diseases such as inflammatory bowel disease (IBD). IBD is a complicated inflammatory colitis disorder; Crohn’s disease and ulcerative colitis are the principal types. Genetic studies have shown the clinical relevance of several autophagy-related genes (ATGs) in the pathogenesis of IBD. Additionally, recent studies using conditional knockout mice have led to a comprehensive understanding of ATGs that affect intestinal inflammation, Paneth cell abnormality and enteric pathogenic infection during colitis. In this review, we discuss the various ATGs involved in macroautophagy and selective autophagy, including ATG16L1, IRGM, LRRK2, ATG7, p62, optineurin and TFEB in the maintenance of intestinal homeostasis. Although advances have been made regarding the involvement of ATGs in maintaining intestinal homeostasis, determining the precise contribution of autophagy has remained elusive. Recent efforts based on direct targeting of ATGs and autophagy will further facilitate the development of new therapeutic opportunities for IBD.
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Orlova E, Yeh A, Shi M, Firek B, Ranganathan S, Whitcomb DC, Finegold DN, Ferrell RE, Barmada MM, Marazita ML, Hinds DA, Shaffer JR, Morowitz MJ. Genetic association and differential expression of PITX2 with acute appendicitis. Hum Genet 2019; 138:37-47. [PMID: 30392061 PMCID: PMC6514078 DOI: 10.1007/s00439-018-1956-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/30/2018] [Indexed: 12/15/2022]
Abstract
Appendicitis affects 9% of Americans and is the most common diagnosis requiring hospitalization of both children and adults. We performed a genome-wide association study of self-reported appendectomy with 18,773 affected adults and 114,907 unaffected adults of European American ancestry. A significant association with appendectomy was observed at 4q25 near the gene PITX2 (rs2129979, p value = 8.82 × 10-14) and was replicated in an independent sample of Caucasians (59 affected, 607 unaffected; p value = 0.005). Meta-analysis of the associated variant across our two cohorts and cohorts from Iceland and the Netherlands (in which this association had previously been reported) showed strong cumulative evidence of association (OR = 1.12; 95% CI 1.09-1.14; p value = 1.81 × 10-23) and some evidence for effect heterogeneity (p value = 0.03). Eight other loci were identified at suggestive significance in the discovery GWAS. Associations were followed up by measuring gene expression across resected appendices with varying levels of inflammation (N = 75). We measured expression of 27 genes based on physical proximity to the GWAS signals, evidence of being targeted by eQTLs near the signals according to RegulomeDB (score = 1), or both. Four of the 27 genes (including PITX2) showed significant evidence (p values < 0.0033) of differential expression across categories of appendix inflammation. An additional ten genes showed nominal evidence (p value < 0.05) of differential expression, which, together with the significant genes, is more than expected by chance (p value = 6.6 × 10-12). PITX2 impacts morphological development of intestinal tissue, promotes an anti-oxidant response, and its expression correlates with levels of intestinal bacteria and colonic inflammation. Further studies of the role of PITX2 in appendicitis are warranted.
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Affiliation(s)
- Ekaterina Orlova
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Andrew Yeh
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Min Shi
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Sarangarajan Ranganathan
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - David C Whitcomb
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
- Department of Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Department of Cell Biology and Molecular Physiology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - David N Finegold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
| | - Robert E Ferrell
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
| | - M Michael Barmada
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | | | - John R Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, 130 De Soto Street, 3131 Parran Hall, Pittsburgh, PA, 15261, USA.
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
- Faculty Pavilion 7th Floor, Children's Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, Pittsburgh, PA, 15224, USA.
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Ajayi TA, Innes CL, Grimm SA, Rai P, Finethy R, Coers J, Wang X, Bell DA, McGrath JA, Schurman SH, Fessler MB. Crohn's disease IRGM risk alleles are associated with altered gene expression in human tissues. Am J Physiol Gastrointest Liver Physiol 2019; 316:G95-G105. [PMID: 30335469 PMCID: PMC6383377 DOI: 10.1152/ajpgi.00196.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Crohn's disease (CD) is a chronic inflammatory gastrointestinal disorder. Genetic association studies have implicated dysregulated autophagy in CD. Among risk loci identified are a promoter single nucleotide polymorphism (SNP)( rs13361189 ) and two intragenic SNPs ( rs9637876 , rs10065172 ) in immunity-related GTPase family M ( IRGM) a gene that encodes a protein of the autophagy initiation complex. All three SNPs have been proposed to modify IRGM expression, but reports have been divergent and largely derived from cell lines. Here, analyzing RNA-Sequencing data of human tissues from the Genotype-Tissue Expression Project, we found that rs13361189 minor allele carriers had reduced IRGM expression in whole blood and terminal ileum, and upregulation in ileum of ZNF300P1, a locus adjacent to IRGM on chromosome 5q33.1 that encodes a long noncoding RNA. Whole blood and ileum from minor allele carriers had altered expression of multiple additional genes that have previously been linked to colitis and/or autophagy. Notable among these was an increase in ileum of LTF (lactoferrin), an established fecal inflammatory biomarker of CD, and in whole blood of TNF, a key cytokine in CD pathogenesis. Last, we confirmed that risk alleles at all three loci associated with increased risk for CD but not ulcerative colitis in a case-control study. Taken together, our findings suggest that genetically encoded IRGM deficiency may predispose to CD through dysregulation of inflammatory gene networks. Gene expression profiling of disease target tissues in genetically susceptible populations is a promising strategy for revealing new leads for the study of molecular pathogenesis and, potentially, for precision medicine. NEW & NOTEWORTHY Single nucleotide polymorphisms in immunity-related GTPase family M ( IRGM), a gene that encodes an autophagy initiation protein, have been linked epidemiologically to increased risk for Crohn's disease (CD). Here, we show for the first time that subjects with risk alleles at two such loci, rs13361189 and rs10065172 , have reduced IRGM expression in whole blood and terminal ileum, as well as dysregulated expression of a wide array of additional genes that regulate inflammation and autophagy.
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Affiliation(s)
- Teminioluwa A. Ajayi
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina,2Duke University School of Medicine, Durham, North Carolina
| | - Cynthia L. Innes
- 3Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Sara A. Grimm
- 4Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Prashant Rai
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Ryan Finethy
- 5Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina
| | - Jörn Coers
- 5Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina
| | - Xuting Wang
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Douglas A. Bell
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | | | - Shepherd H. Schurman
- 3Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Michael B. Fessler
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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Juyal G, Sood A, Midha V, Thelma BK. Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018; 97:1493-1507. [PMID: 30555100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ulcerative colitis (UC), one of the two clinical subtypes of inflammatory bowel disease is perceived as a potential 'sleeping giant' in the Indian subcontinent. Clinical manifestation is overall believed to be the same across ethnic groups but overwhelming genetics from large European and fewer non-European studies have revealed shared as well as unique disease susceptibly signaturesbetween them, pointing to population specific differences at genomic and environmental levels. A systematic recount of the four major eras in UC genetics spanning earliest linkage analysis, cherry picked candidate gene association studies, unbiased genomewide association studies, their logical extension in trans-ethnic setting (Immunochip study), lastly whole exome sequencing efforts forrare variant burden; and lessons learnt thereof in context of genetically distinct Indian population was attempted in this review. Genetic heterogeneity manifesting at allelic/locus level across these approaches has been the consistent finding through the range of pan India studies. On the other hand, these salient findings also highlight the limitations of even the best of these genetic leadsfor prognostic/clinical application. The imminent need, therefore, for the UC research community to adopt newer approaches/tools with improved study design to (i) gain better insight into genetic/mechanistic basis of disease; (ii) identify biomarkers of immediate translational value; and (iii) develop new/alternate therapeutic options is emphasized at the end.
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Affiliation(s)
- Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India. ,
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40
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Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018. [DOI: 10.1007/s12041-018-1015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Brown MA, Wordsworth BP. Genetics in ankylosing spondylitis - Current state of the art and translation into clinical outcomes. Best Pract Res Clin Rheumatol 2018; 31:763-776. [PMID: 30509439 DOI: 10.1016/j.berh.2018.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 12/20/2022]
Abstract
Ankylosing spondylitis (AS) is the prototypic form of axial spondyloarthritis (axSpA). It is highly heritable, with studies conducted in twins and in unrelated cases and controls showing that the heritability for AS is much higher than those for inflammatory bowel disease or rheumatoid arthritis. To date, 116 loci have been identified, contributing to 28% of the genetic variation in the disease. These loci provide important clues into pathogenic pathways in the disease that have led to therapeutic advances such as the repositioning of IL-17 inhibitors in the disease. Much more research is currently required to determine the functional mechanisms by which the genetic associations operate, from which it is likely that novel therapeutic approaches will be developed.
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Affiliation(s)
- Matthew A Brown
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Brisbane, Australia.
| | - B Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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Zhang H, Zeng Z, Mukherjee A, Shen B. Molecular diagnosis and classification of inflammatory bowel disease. Expert Rev Mol Diagn 2018; 18:867-886. [PMID: 30152711 DOI: 10.1080/14737159.2018.1516549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Traditional diagnosis and classification of inflammatory bowel diseases (IBDs) have been based on clinical evaluation, laboratory testing, endoscopy, imaging, and histological examinations. With the advancement of medical technology, an increasing number of molecular surrogates are playing a key role in diagnosis, differential diagnosis, assessment of disease activity, prediction of clinical course, and therapeutic response of IBD. Areas covered: The authors review roles of both existing and emerging surrogates including genetic, serological, histologic, and fecal markers in diagnosis and classification of IBD. Comparisons in advantages and disadvantages of different markers have also been discussed. In addition, this review underscores controversial and unclear aspects which need further study. Expert commentary: IBD is characteristic of chronicity, relapse-remission and destructiveness. It is of great importance for clinicians to make an accurate diagnosis and classification. Current and new molecular markers perform well with acceptable sensitivity and specificity. The use of molecular markers in clinical practice needs to be further explored and then generalized. More work is warranted to identify novel useful markers and elucidate how to apply them together with current markers in clinical settings.
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Affiliation(s)
- Hu Zhang
- a Center for Inflammatory Bowel Disease & Department of Gastroenterology , West China Hospital, Sichuan University , Chengdu , China
| | - Zhen Zeng
- a Center for Inflammatory Bowel Disease & Department of Gastroenterology , West China Hospital, Sichuan University , Chengdu , China
| | - Arjudeb Mukherjee
- b West China School of Medicine , Sichuan University , Chengdu , China
| | - Bo Shen
- c Center for Inflammatory Bowel Disease, Digestive Disease and Surgery Institute, The Cleveland Clinic Foundation , Cleveland , Ohio , USA
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Li Z, Wang Y, Zhu Y. Association of miRNA-146a rs2910164 and miRNA-196 rs11614913 polymorphisms in patients with ulcerative colitis: A meta-analysis and review. Medicine (Baltimore) 2018; 97:e12294. [PMID: 30278502 PMCID: PMC6181578 DOI: 10.1097/md.0000000000012294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND It has been reported that the single nucleotide polymorphisms (SNPs) miRNA-196 (miR-196) rs11614913 and miRNA-146a (miR-146a) rs2910164 are related to susceptibility to ulcerative colitis (UC). Because the previously reported results have been mixed and uncertain, the aim of this study was to perform a meta-analysis and review to assess the relationship between these 2 SNPs and UC risk. METHODS In this analysis, 5 studies involving 1023 cases and 1769 controls for miR-196 rs11614913 and 4 studies involving 827 cases and 1451 controls for miR-146 rs2910164 were included. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were used to pool the effect size. RESULTS A decreased risk of UC was identified in homozygote comparison (GG vs CC: OR = 0.69, 95% CI: 0.52-0.93, P = .02), recessive comparison (GG vs CG + CC: OR = 0.74, 95% CI: 0.59-0.92, P = .007), and dominant comparison (GG + CG vs CC: OR = 0.79, 95% CI: 0.65-0.97, P = .02) of miR-146 rs2910164 in Asian but not Caucasian population. No evidence of an association was shown between the rs11614913 polymorphism and UC risk in allelic, heterozygote, homozygote, recessive, and dominant models in both Caucasian and Asian populations (P > .05). CONCLUSIONS MiR-146 rs2910164, but not miR-196 rs11614913, was associated with a decreased risk of UC in Asian population. However, the results should be treated with caution because of the limited sample size and heterogeneity. Well-designed studies with large sample sizes and more ethnic groups are needed to validate the risks identified in the current meta-analysis and review.
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Affiliation(s)
- Zhongyi Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University
| | - Yao Wang
- Department of Epidemiology, Medical School of Jinan University, Guangzhou, Guangdong Province
| | - Yi Zhu
- Department of Gastroenterological Surgery, First Hospital of Jiaxing, Jiaxing, Zhejiang, China
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Hargarten JC, Williamson PR. Epigenetic Regulation of Autophagy: A Path to the Control of Autoimmunity. Front Immunol 2018; 9:1864. [PMID: 30154791 PMCID: PMC6102341 DOI: 10.3389/fimmu.2018.01864] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
Autoimmune diseases are a significant cause of debilitation and mortality globally and are in need of cost-effective therapeutics. Autophagy is a cellular pathway that facilitates immune modulation involved in both pathogen control and autoimmunity. Regulation is multifactorial and includes a number of epigenetic pathways which can involve modification of DNA-binding histones to induce autophagy-related mRNA synthesis or microRNA and decapping-associated mRNA degradation which results in autophagy suppression. Appreciation of epigenetic-based pathways involved in autophagy and autoimmunity may facilitate application of a burgeoning group of epigenetic pharmaceuticals to these important diseases.
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Affiliation(s)
- Jessica C Hargarten
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Peter R Williamson
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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Moon CM, Kim SW, Ahn JB, Ma HW, Che X, Kim TI, Kim WH, Cheon JH. Deep Resequencing of Ulcerative Colitis-Associated Genes Identifies Novel Variants in Candidate Genes in the Korean Population. Inflamm Bowel Dis 2018; 24:1706-1717. [PMID: 29733354 DOI: 10.1093/ibd/izy122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND Genome-wide association studies and meta-analyses have revealed the genetic background of ulcerative colitis (UC) by identifying common variants. However, these variants do not fully explain the disease variance in UC. To identify novel variants, we performed deep resequencing of UC-associated genes in Korean UC patients and subsequently investigated the functional roles of identified susceptibility genes. METHODS We performed targeted deep resequencing of 108 genes in 24 Korean UC patients and then performed association analysis with data from 126 healthy controls. We validated these variants using 2-stage replication studies including 793 UC patients and 783 controls. We performed in silico and pathway analyses and functional analyses. RESULTS The combined analysis including 2 replication studies identified 6 novel susceptibility loci and reconfirmed 10 previously reported loci. Among the novel single nucleotide variants (SNVs), rs10035653 in C5orf55 (P = 2.08 × 10-3; OR = 1.50), rs41417449 in BTNL2 (P = 1.27 × 10-2; OR = 1.32), rs3117099 in HCG23 (P = 9.98 × 10-6; OR = 1.40), rs7192 in HLA-DRA (P = 6.95 × 10-9; OR = 1.57), and rs3744246 in ORMDL3 (P = 2.21 × 10-2; OR = 1.21) were identified as causal variants, whereas rs713669 in IL17REL (P = 2.69 × 10-2; OR = 0.84) as a protective variant for UC. When correcting multiple testing, 3 novel SNVs (rs41417449 in BTNL2, rs3744246 in ORMDL3, and rs713669 in IL17REL) and 4 previously reported SNVs did not reach a statistical significance. Functional study suggested that SNVs of BTNL2 and C5orf55 exacerbated the inflammatory response both in vitro and in vivo. CONCLUSIONS This study identified 3 novel susceptibility loci and validated 6 previously reported SNVs for UC through deep resequencing in Koreans and revealed the functional roles of BTNL2 and C5orf55.
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Affiliation(s)
- Chang Mo Moon
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Won Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Bum Ahn
- Department of Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Woo Ma
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Xiumei Che
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Ho Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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Imam T, Park S, Kaplan MH, Olson MR. Effector T Helper Cell Subsets in Inflammatory Bowel Diseases. Front Immunol 2018; 9:1212. [PMID: 29910812 PMCID: PMC5992276 DOI: 10.3389/fimmu.2018.01212] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/15/2018] [Indexed: 12/30/2022] Open
Abstract
The gastrointestinal tract is a site of high immune challenge, as it must maintain a delicate balance between tolerating luminal contents and generating an immune response toward pathogens. CD4+ T cells are key in mediating the host protective and homeostatic responses. Yet, CD4+ T cells are also known to be the main drivers of inflammatory bowel disease (IBD) when this balance is perturbed. Many subsets of CD4+ T cells have been identified as players in perpetuating chronic intestinal inflammation. Over the last few decades, understanding of how each subset of Th cells plays a role has dramatically increased. Simultaneously, this has allowed development of therapeutic innovation targeting specific molecules rather than broad immunosuppressive agents. Here, we review the emerging evidence of how each subset functions in promoting and sustaining the chronic inflammation that characterizes IBD.
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Affiliation(s)
- Tanbeena Imam
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Sungtae Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Mark H Kaplan
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Matthew R Olson
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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Wang MJ, Xu XL, Yao GL, Yu Q, Zhu CF, Kong ZJ, Zhao H, Tang LM, Qin XH. MYO9B gene polymorphisms are associated with the risk of inflammatory bowel diseases. Oncotarget 2018; 7:58862-58875. [PMID: 27556856 PMCID: PMC5312281 DOI: 10.18632/oncotarget.11186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/19/2016] [Indexed: 12/19/2022] Open
Abstract
Myosin IXB (MYO9B) gene polymorphisms have been extensively investigated in terms of their associations with inflammatory bowel disease (IBD), with contradictory results. The aim of this meta-analysis was to evaluate associations between MY09B gene polymorphisms and the risk of IBD, Crohn's disease (CD) and ulcerative colitis (UC). Eligible studies from PubMed, Embase, and CNKI databases were identified. Pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. Ten studies published in eight papers reporting 8,975 cases and 9,482 controls were included in this meta-analysis. Five MY09B gene polymorphisms were evaluated: rs1545620, rs962917, rs1457092, rs2305764, and rs2305767. Our data suggested that the rs1545620 polymorphism was associated with a decreased risk of IBD. A similar result was found for rs2305767 and UC. The rs962917 single nucleotide polymorphism (SNP) increased the risk of IBD, CD and UC. Moreover, rs1457092 increased the risk of IBD and UC. Rs2305764 was also associated with an increased risk of IBD. Furthermore, stratification analyses indicated that rs1545620 decreased the risk of IBD, while rs962917 increased the risk of IBD, CD and UC in Caucasian populations. To sum up, our data indicate that these five SNPs in MY09B are significantly associated with the risk of IBD.
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Affiliation(s)
- Ming-Jie Wang
- Department of Orthopedics, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
| | - Xiao-Liang Xu
- Liver Surgery of Jiangsu Province People's Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Guo-Liang Yao
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiang Yu
- Department of General Surgery, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
| | - Chun-Fu Zhu
- Department of General Surgery, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
| | - Zhi-Jun Kong
- Department of General Surgery, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
| | - Hui Zhao
- Department of General Surgery, Wuxi Third People's Hospital, Wuxi, China
| | - Li-Ming Tang
- Department of General Surgery, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
| | - Xi-Hu Qin
- Department of General Surgery, Affiliated Hospital of Nanjing Medical University, Changzhou Second People's Hospital, Changzhou, China
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Iwamoto T, Yashima K, Morio K, Ueda N, Ikebuchi Y, Kawaguchi K, Harada K, Isomoto H. Association of Clinical Features with Human Leukocyte Antigen in Japanese Patients with Ulcerative Colitis. Yonago Acta Med 2018. [DOI: 10.33160/yam.2018.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Taku Iwamoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kazuo Yashima
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Keiko Morio
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Naoki Ueda
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Yuichiro Ikebuchi
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Koichiro Kawaguchi
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Kenichi Harada
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Hajime Isomoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
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A cellular and molecular view of T helper 17 cell plasticity in autoimmunity. J Autoimmun 2017; 87:1-15. [PMID: 29275836 DOI: 10.1016/j.jaut.2017.12.007] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023]
Abstract
Since the original identification of the T helper 17 (Th17) subset in 2005, it has become evident that these cells do not only contribute to host defence against pathogens, such as bacteria and fungi, but that they are also critically involved in the pathogenesis of many autoimmune diseases. In contrast to the classic Th1 and Th2 cells, which represent rather stably polarized subsets, Th17 cells display remarkable heterogeneity and plasticity. This has been attributed to the characteristics of the key transcription factor that guides Th17 differentiation, retinoic acid receptor-related orphan nuclear receptor gamma (RORγ). Unlike the 'master regulators' T-bet and GATA3 that orchestrate Th1 and Th2 differentiation, respectively, RORγ controls transcription at relatively few loci in Th17 cells. Moreover, its expression is not stabilized by positive feedback loops but rather influenced by environmental cues, allowing for substantial functional plasticity. Importantly, a subset of IL-17/IFNγ double-producing Th17 cells was identified in both human and mouse models. Evidence is accumulating that these IL-17/IFNγ double-producing cells are pathogenic drivers in autoimmune diseases, including rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease. In addition, IL-17/IFNγ double-producing cells have been identified in disorders in which the role of autoimmunity remains unclear, such as sarcoidosis. The observed plasticity of Th17 cells towards the Th1 phenotype can be explained by extensive epigenetic priming of the IFNG locus in Th17 cells. In fact, Th17 cells display an IFNG chromatin landscape that is remarkably similar to that of Th1 cells. On the other hand, pathogenic capabilities of Th17 cells can be restrained by stimulating IL-10 production and transdifferentiation into IL-10 producing T regulatory type 1 (Tr1) cells. In this review, we discuss recent advances in our knowledge on the cellular and molecular mechanisms involved in Th17 differentiation, heterogeneity and plasticity. We focus on transcriptional regulation of the Th17 expression program, the epigenetic dynamics involved, and how genetic variants associated with autoimmunity may affect immune responses through distal gene regulatory elements. Finally, the implications of Th17 cell plasticity for the pathogenesis and treatment of human autoimmune diseases will be discussed.
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Tian T, Wang Z, Zhang J. Pathomechanisms of Oxidative Stress in Inflammatory Bowel Disease and Potential Antioxidant Therapies. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:4535194. [PMID: 28744337 PMCID: PMC5506473 DOI: 10.1155/2017/4535194] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 05/22/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal disease whose incidence has risen worldwide in recent years. Accumulating evidence shows that oxidative stress plays an essential role in the pathogenesis and progression of IBD. This review highlights the generation of reactive oxygen species (ROS) and antioxidant defense mechanisms in the gastrointestinal (GI) tract, the involvement of oxidative stress signaling in the initiation and progression of IBD and its relationships with genetic susceptibility and the mucosal immune response. In addition, potential therapeutic strategies for IBD that target oxidative stress signaling are reviewed and discussed. Though substantial progress has been made in understanding the role of oxidative stress in IBD in humans and experimental animals, the underlying mechanisms are still not well defined. Thus, further studies are needed to validate how oxidative stress signaling is involved in and contributes to the development of IBD.
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Affiliation(s)
- Tian Tian
- College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Ziling Wang
- College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
| | - Jinhua Zhang
- College of Life Science and Bioengineering, Beijing Jiaotong University, Beijing 100044, China
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