1
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Malignancies in Patients with Celiac Disease: Diagnostic Challenges and Molecular Advances. Genes (Basel) 2023; 14:genes14020376. [PMID: 36833303 PMCID: PMC9956047 DOI: 10.3390/genes14020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Celiac disease (CD) is a multiorgan autoimmune disorder of the chronic intestinal disease group characterized by duodenal inflammation in genetically predisposed individuals, precipitated by gluten ingestion. The pathogenesis of celiac disease is now widely studied, overcoming the limits of the purely autoimmune concept and explaining its hereditability. The genomic profiling of this condition has led to the discovery of numerous genes involved in interleukin signaling and immune-related pathways. The spectrum of disease manifestations is not limited to the gastrointestinal tract, and a significant number of studies have considered the possible association between CD and neoplasms. Patients with CD are found to be at increased risk of developing malignancies, with a particular predisposition of certain types of intestinal cancer, lymphomas, and oropharyngeal cancers. This can be partially explained by common cancer hallmarks present in these patients. The study of gut microbiota, microRNAs, and DNA methylation is evolving to find the any possible missing links between CD and cancer incidence in these patients. However, the literature is extremely mixed and, therefore, our understanding of the biological interplay between CD and cancer remains limited, with significant implications in terms of clinical management and screening protocols. In this review article, we seek to provide a comprehensive overview of the genomics, epigenomics, and transcriptomics data on CD and its relation to the most frequent types of neoplasms that may occur in these patients.
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2
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Romero-Garmendia I. Separation of epithelial and immune cells from biopsy samples. Methods Cell Biol 2023; 179:59-68. [PMID: 37625880 DOI: 10.1016/bs.mcb.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Celiac disease (CD) is a chronic and autoimmune disease that develops in genetically predisposed individuals upon exposure to dietary gluten. The availability of the target tissue for research has made it possible to identify alterations in the transcriptome and methylome in the celiac gut. However, gene expression and methylation is highly variable among different cell types, and separation of cellular populations in target tissue must be considered for the understanding of the specific cellular and immune responses to gluten. In this context, a few studies have demonstrated that focusing on an isolated cell population, novel candidate genes involved in the pathogenesis of the disease can be identified. Here, we describe a method to separate epithelial and immune cells from biopsy samples for DNA and RNA isolation. With minor variations, the same technique can be applied to other tissues and cell types.
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Affiliation(s)
- Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.
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3
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Functional implications of the CpG island methylation in the pathogenesis of celiac disease. Mol Biol Rep 2022; 49:10051-10064. [PMID: 35633417 DOI: 10.1007/s11033-022-07585-w] [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: 01/29/2022] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
Abstract
Investigation of gene-environment cross talk through epigenetic modifications led to better understanding of the number of complex diseases. Clinical heterogeneity and differential treatment response often contributed by the epigenetic signatures which could be personal. DNA methylation at CpG islands presents a critical nuclear process as a result of gene-environment interactions. These CpG islands are frequently present near the promoter sequence of genes and get differentially methylated under specific environmental conditions. Technical advancements facilitate in high throughput screening of differentially methylated CpG islands. Recent epigenetic studies unraveled several CD susceptibility genes expressed in peripheral blood lymphocytes (PBLs), duodenal mucosa, lamina and epithelial cells that are influenced by differentially methylated CpG islands. Here we highlighted these susceptibility genes; classify these genes based on cellular functions and tissue of expression. We further discussed how these genes interacts with each other to influence critical pathways like NF-κB signaling pathway, IL-17 signaling cascade, RIG-I like receptor signaling pathway, NOD-like receptor pathways among several others. This review also shed light on how gut microbiota may lead to the differential methylation of CpG islands of CD susceptibility genes. Large scale epigenetic studies followed by estimation of heritability of these CpG methylation and polygenic risk score estimation of these genes would prioritize potentially druggable targets for better therapeutics. In vivo studies are warranted to unravel further cellular responses to CpG methylation.
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4
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Auricchio R, Calabrese I, Galatola M, Cielo D, Carbone F, Mancuso M, Matarese G, Troncone R, Auricchio S, Greco L. Gluten consumption and inflammation affect the development of celiac disease in at-risk children. Sci Rep 2022; 12:5396. [PMID: 35354862 PMCID: PMC8968719 DOI: 10.1038/s41598-022-09232-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/11/2022] [Indexed: 12/20/2022] Open
Abstract
Gene expression, lipidomic and growth impairment findings suggest that the natural history of celiac disease (CD) starts before the gluten-induced immune response. Gluten intake in the first years of life is a controversial risk factor. We aimed to estimate the risk of developing CD associated with the amount of gluten intake and the serum inflammatory profile in genetically predisposed infants. From an Italian cohort of children at risk for CD, we enrolled 27 children who developed CD (cases) and 56 controls matched by sex and age. A dietary interview at 9, 12, 18, 24 and 36 months was performed. Serum cytokines (INFγ, IL1β, IL2, IL4, IL6, IL10 IL12p70, IL17, and TNFα) were analysed at 4 and 36 months. Infants who developed CD by 6 years showed an increase in serum cytokines (INFγ, IL1β, IL2, IL6, IL10, IL12p70 and TNFα) at 4 months of age before gluten introduction. CD cases ate significantly more gluten in the second year of life than controls, and gluten intake in the second year of life was strongly correlated with serum cytokines (INFγ, IL2, IL4, IL12p70, IL17) at 36 months only in CD cases. The dietary pattern of infants who developed CD was characterized by high consumption of biscuits and fruit juices and low intake of milk products, legumes, vegetables and fruits. Genetically predisposed infants who developed CD showed a unique serum cytokine profile at 4 months before gluten consumption. The amount of gluten was strongly correlated with an inflammatory profile in serum cytokines at 36 months only in infants who developed CD.
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Affiliation(s)
- Renata Auricchio
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131, Naples, Italy. .,European Laboratory for Food Induced Diseases, University Federico II, Via S. Pansini 5, 80131, Naples, Italy.
| | - Ilaria Calabrese
- Department of Clinical Medicine and Surgery, University Federico II, Naples, Italy
| | - Martina Galatola
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Donatella Cielo
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Fortunata Carbone
- Laboratory of Immunology, Institute for Experimental Endocrinology and Oncology, National Research Council (IEOS-CNR), Naples, Italy.,Neuroimmunology Unit, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Marianna Mancuso
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Giuseppe Matarese
- Laboratory of Immunology, Institute for Experimental Endocrinology and Oncology, National Research Council (IEOS-CNR), Naples, Italy.,Department of Molecular Medicine and Medical Biotechnology, University Federico II, Naples, Italy
| | - Riccardo Troncone
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131, Naples, Italy.,European Laboratory for Food Induced Diseases, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Salvatore Auricchio
- European Laboratory for Food Induced Diseases, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Luigi Greco
- European Laboratory for Food Induced Diseases, University Federico II, Via S. Pansini 5, 80131, Naples, Italy
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5
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Shyamala N, Kongettira CL, Puranam K, Kupsal K, Kummari R, Padala C, Hanumanth SR. In silico identification of single nucleotide variations at CpG sites regulating CpG island existence and size. Sci Rep 2022; 12:3574. [PMID: 35246549 PMCID: PMC8897451 DOI: 10.1038/s41598-022-05198-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/03/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic and epigenetic modifications of genes involved in the key regulatory pathways play a significant role in the pathophysiology and progression of multifactorial diseases. The present study is an attempt to identify single nucleotide variations (SNVs) at CpG sites of promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes influencing CpG island (CGI) existence and size associated with the pathophysiology of Diabetes mellitus, Coronary artery disease and Cancers. Promoter sequences located between -2000 to + 2000 bp were retrieved from the EPDnew database and predicted the CpG island using MethPrimer. Further, SNVs at CpG sites were accessed from NCBI, Ensembl while transcription factor (TF) binding sites were accessed using AliBaba2.1. CGI existence and size were determined for each SNV at CpG site with respect to wild type and variant allele by MethPrimer. A total of 200 SNVs at CpG sites were analyzed from the promoters of ACAT1, APOB, APOE, CYBA, FAS, FLT1, KSR2, LDLR, MMP9, PCSK9, PHOX2A, REST, SH2B3, SORT1 and TIMP1 genes. Of these, only 17 (8.5%) SNVs were found to influence the loss of CGI while 70 (35%) SNVs were found to reduce the size of CGI. It has also been found that 59% (10) of CGI abolishing SNVs are showing differences in binding of TFs. The findings of the study suggest that the candidate SNVs at CpG sites regulating CGI existence and size might influence the DNA methylation status and expression of genes involved in molecular pathways associated with several diseases. The insights of the present study may pave the way for new experimental studies to undertake challenges in DNA methylation, gene expression and protein assays.
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Affiliation(s)
- Nivas Shyamala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chaitra Lava Kongettira
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Kaushik Puranam
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Keerthi Kupsal
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Ramanjaneyulu Kummari
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
| | - Chiranjeevi Padala
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana State, India
| | - Surekha Rani Hanumanth
- Department of Genetics and Biotechnology, University College of Science, Osmania University, Hyderabad, 500007, Telangana State, India.
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6
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Gnodi E, Meneveri R, Barisani D. Celiac disease: From genetics to epigenetics. World J Gastroenterol 2022; 28:449-463. [PMID: 35125829 PMCID: PMC8790554 DOI: 10.3748/wjg.v28.i4.449] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/16/2021] [Accepted: 01/11/2022] [Indexed: 02/06/2023] Open
Abstract
Celiac disease (CeD) is a multifactorial autoimmune disorder spread worldwide. The exposure to gluten, a protein found in cereals like wheat, barley and rye, is the main environmental factor involved in its pathogenesis. Even if the genetic predisposition represented by HLA-DQ2 or HLA-DQ8 haplotypes is widely recognised as mandatory for CeD development, it is not enough to explain the total predisposition for the disease. Furthermore, the onset of CeD comprehend a wide spectrum of symptoms, that often leads to a delay in CeD diagnosis. To overcome this deficiency and help detecting people with increased risk for CeD, also clarifying CeD traits linked to disease familiarity, different studies have tried to make light on other predisposing elements. These were in many cases genetic variants shared with other autoimmune diseases. Since inherited traits can be regulated by epigenetic modifications, also induced by environmental factors, the most recent studies focused on the potential involvement of epigenetics in CeD. Epigenetic factors can in fact modulate gene expression with many mechanisms, generating more or less stable changes in gene expression without affecting the DNA sequence. Here we analyze the different epigenetic modifications in CeD, in particular DNA methylation, histone modifications, non-coding RNAs and RNA methylation. Special attention is dedicated to the additional predispositions to CeD, the involvement of epigenetics in developing CeD complications, the pathogenic pathways modulated by epigenetic factors such as microRNAs and the potential use of epigenetic profiling as biomarker to discriminate different classes of patients.
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Affiliation(s)
- Elisa Gnodi
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
| | - Raffaella Meneveri
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
| | - Donatella Barisani
- School of Medicine and Surgery, University of Milano-Bicocca, Monza 20900, Italy
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7
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Brown JA, Sanidad KZ, Lucotti S, Lieber CM, Cox RM, Ananthanarayanan A, Basu S, Chen J, Shan M, Amir M, Schmidt F, Weisblum Y, Cioffi M, Li T, Rowdo FM, Martin ML, Guo CJ, Lyssiotis C, Layden BT, Dannenberg AJ, Bieniasz PD, Lee B, Inohara N, Matei I, Plemper RK, Zeng MY. Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection. Gut Microbes 2022; 14:2105609. [PMID: 35915556 PMCID: PMC9348133 DOI: 10.1080/19490976.2022.2105609] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome is intricately coupled with immune regulation and metabolism, but its role in Coronavirus Disease 2019 (COVID-19) is not fully understood. Severe and fatal COVID-19 is characterized by poor anti-viral immunity and hypercoagulation, particularly in males. Here, we define multiple pathways by which the gut microbiome protects mammalian hosts from SARS-CoV-2 intranasal infection, both locally and systemically, via production of short-chain fatty acids (SCFAs). SCFAs reduced viral burdens in the airways and intestines by downregulating the SARS-CoV-2 entry receptor, angiotensin-converting enzyme 2 (ACE2), and enhancing adaptive immunity via GPR41 and 43 in male animals. We further identify a novel role for the gut microbiome in regulating systemic coagulation response by limiting megakaryocyte proliferation and platelet turnover via the Sh2b3-Mpl axis. Taken together, our findings have unraveled novel functions of SCFAs and fiber-fermenting gut bacteria to dampen viral entry and hypercoagulation and promote adaptive antiviral immunity.
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Affiliation(s)
- Julia A. Brown
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Katherine Z. Sanidad
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Serena Lucotti
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Carolin M. Lieber
- Institute for Biomedical Sciences, Georgia State University; Atlanta, GA, United States of America
| | - Robert M. Cox
- Institute for Biomedical Sciences, Georgia State University; Atlanta, GA, United States of America
| | - Aparna Ananthanarayanan
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Srijani Basu
- Department of Medicine, Weill Cornell Medicine; New York, NY, United States of America
| | - Justin Chen
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
| | - Mengrou Shan
- Rogel Cancer Center, University of Michigan; Ann Arbor, MI, United States of America
| | - Mohammed Amir
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University; New York, NY, United States of America
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University; New York, NY, United States of America
| | - Michele Cioffi
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Tingting Li
- Jill Roberts Institute for Inflammatory Bowel Disease, Weill Cornell Medicine; New York, NY, United States of America
| | - Florencia Madorsky Rowdo
- Englander Institute for Precision Medicine, Weill Cornell Medicine; New York, NY, United States of America
| | - M. Laura Martin
- Englander Institute for Precision Medicine, Weill Cornell Medicine; New York, NY, United States of America
| | - Chun-Jun Guo
- Jill Roberts Institute for Inflammatory Bowel Disease, Weill Cornell Medicine; New York, NY, United States of America
| | - Costas Lyssiotis
- Department of Medicine, Weill Cornell Medicine; New York, NY, United States of America
| | - Brian T. Layden
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago; Chicago, Illinois, United States of America
- Jesse Brown Veterans Affairs Medical Center; Chicago, Illinois, United States of America
| | - Andrew J. Dannenberg
- Department of Medicine, Weill Cornell Medicine; New York, NY, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University; New York, NY, United States of America
- Howard Hughes Medical Institute, The Rockefeller University; New York, NY, United States of America
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai; New York, NY, United States of America
| | - Naohiro Inohara
- Rogel Cancer Center, University of Michigan; Ann Arbor, MI, United States of America
| | - Irina Matei
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University; Atlanta, GA, United States of America
| | - Melody Y. Zeng
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine; New York, NY, USA
- Department of Pediatrics, Weill Cornell Medicine; New York, NY, United States of America
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8
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Verdu EF, Schuppan D. Co-factors, Microbes, and Immunogenetics in Celiac Disease to Guide Novel Approaches for Diagnosis and Treatment. Gastroenterology 2021; 161:1395-1411.e4. [PMID: 34416277 DOI: 10.1053/j.gastro.2021.08.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022]
Abstract
Celiac disease (CeD) is a frequent immune-mediated disease that affects not only the small intestine but also many extraintestinal sites. The role of gluten proteins as dietary triggers, HLA-DQ2 or -DQ8 as major necessary genetic predisposition, and tissue transglutaminase (TG2) as mechanistically involved autoantigen, are unique features of CeD. Recent research implicates many cofactors working in synergism with these key triggers, including the intestinal microbiota and their metabolites, nongluten dietary triggers, intestinal barrier defects, novel immune cell phenotypes, and mediators and cytokines. In addition, apart from HLA-DQ2 and -DQ8, multiple and complex predisposing genetic factors and interactions have been defined, most of which overlap with predispositions in other, usually autoimmune, diseases that are linked to CeD. The resultant better understanding of CeD pathogenesis, and its manifold manifestations has already paved the way for novel therapeutic approaches beyond the lifelong strict gluten-free diet, which poses a burden to patients and often does not lead to complete mucosal healing. Thus, supported by improved mouse models for CeD and in vitro organoid cultures, several targeted therapies are in phase 2-3 clinical studies, such as highly effective gluten-degrading oral enzymes, inhibition of TG2, cytokine therapies, induction of tolerance to gluten ingestion, along with adjunctive and preventive approaches using beneficial probiotics and micronutrients. These developments are supported by novel noninvasive markers of CeD severity and activity that may be used as companion diagnostics, allow easy-to perform and reliable monitoring of patients, and finally support personalized therapy for CeD.
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Affiliation(s)
- Elena F Verdu
- Division of Gastroenterology, Department of Internal Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Detlef Schuppan
- Institute of Translational Immunology,Research Center for Immune Therapy and Celiac Center, University Medical Center, Johannes Gutenberg University, Mainz, Germany; Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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9
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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10
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Iervasi E, Auricchio R, Strangio A, Greco L, Saverino D. Serum IL-21 levels from celiac disease patients correlates with anti-tTG IgA autoantibodies and mucosal damage. Autoimmunity 2020; 53:225-230. [PMID: 32157915 DOI: 10.1080/08916934.2020.1736047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Objectives: Coeliac disease is a multifactorial disorder influenced by environmental, genetic and immunological factors. Interleukin (IL)-21 has been linked to an increase disease risk and the serum level of IL-21 seems to be increased in CD compared to a healthy control population.Methods: Sera were collected from 160 CD patients, 120 untreated and 40 following a gluten-free diet, and form 45 healthy subjects. Serum IL-21 was evaluated by specific ELISA tests.Results: Our data show that patients with untreated CD display IL-21 concentrations significantly higher than both treated-CD patients (following a gluten-free diet) and controls. In addition, serum IL-21 correlates with serum titres of anti-tTG IgA autoantibodies. Finally, our results show a correlation of this cytokine with duodenal mucosal damage.Conclusions: A role of gluten, as antigen with stimulatory function on IL-21 production, seems to be confirmed by the longitudinal analyses showing that the gluten-free diet decreases to a nearly undetectable amount this cytokine. In addition, the finding of a positive correlation between the serum amount of IL-21 and the grade of duodenal mucosa damage suggests a strong immunomodulatory effect of this cytokine on cytotoxic T lymphocyte functions. This study provides an extra evidence to emerging data on the potential role IL-21 in CD pathogenesis, suggesting its involvement in the development and progression of CD. Significance statement: In untreated CD, serum IL-21 shows higher levels compared with treated CD and healthy subjects. Serum amounts of IL-21 correlate with anti-tTG IgA autoantibodies and with duodenal mucosa damage.
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Affiliation(s)
- Erika Iervasi
- Department of Experimental Medicine, University of Genova, Genova, Italy.,Laboratory of Autoimmunology, Ospedale Policlinico San Martino, Largo Rosanna Benzi, Genova, Italy
| | - Renata Auricchio
- Department of Translational Medical Science, University of Naples Federico II, Napoli, Italy.,European Laboratory for Food-Induced disease (ELFID), University of Naples Federico II, Napoli, Italy
| | - Antonella Strangio
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | - Luigi Greco
- Department of Translational Medical Science, University of Naples Federico II, Napoli, Italy.,European Laboratory for Food-Induced disease (ELFID), University of Naples Federico II, Napoli, Italy
| | - Daniele Saverino
- Department of Experimental Medicine, University of Genova, Genova, Italy.,Laboratory of Autoimmunology, Ospedale Policlinico San Martino, Largo Rosanna Benzi, Genova, Italy
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11
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Khalkhal E, Nobakht F, Haidari MH, Razaghi Z, Ghasemzad M, Sheikhan M, Rostami Nejad M. Evaluation of expression of common genes in the intestine and peripheral blood mononuclear cells (PBMC) associated with celiac disease. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:S60-S67. [PMID: 33585005 PMCID: PMC7881404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AIM this study was conducted to investigate expression of the genes associated with CD in the target tissue in order to estimate contribution of each single gene to development of immune response. Then, the same set of genes was evaluated in peripheral blood mononuclear cells (PBMCs). BACKGROUND Celiac disease (CD) is a chronic systemic autoimmune disease of the small intestine occurring in genetically-susceptible individuals. There are several genes related to immune response. METHODS For this purpose, the genes related to CD were extracted from public databases (documents of proteomics and microarray-based techniques) and were organized in a protein-protein interaction network using the search tool for retrieval of interacting genes/proteins (STRING) database as a plugin of Cytoscape software version 3.6.0. The main genes were introduced and enriched via ClueGO to find the related biochemical pathways. The network was analyzed, and the most important genes were introduced based on central indices. RESULTS Among 20 CD genes as hub and bottleneck nodes, there were 7 genes with common expression in blood and intestinal tissue (C-X-C motif chemokine 11(CXCL11), granzyme B (GZMB), interleukin 15(IL-15), interleukin 17(IL-17A), interleukin 23(IL-23A), t-box transcription factor 21(TBX21), and tumor necrosis factor alpha-induced protein 3(TNFAIP3)). CONCLUSION The enriched biological process related to the central nodes of celiac network indicated that most of hub-bottleneck genes are the well-known ones involved in different types of autoimmune and inflammatory diseases.
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Affiliation(s)
- Ensieh Khalkhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Nobakht
- Chemical Injuries Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossain Haidari
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Ghasemzad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Melika Sheikhan
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami Nejad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Auricchio R, Galatola M, Cielo D, Amoresano A, Caterino M, De Vita E, Illiano A, Troncone R, Greco L, Ruoppolo M. A Phospholipid Profile at 4 Months Predicts the Onset of Celiac Disease in at-Risk Infants. Sci Rep 2019; 9:14303. [PMID: 31586100 PMCID: PMC6778072 DOI: 10.1038/s41598-019-50735-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Celiac disease (CeD) is a multifactorial disease influenced by both genetic and environmental risk factors. CeD genetic components are mainly due to HLA class II genes, which account for approximately 40% of the disease heritability. The environmental factor is linked to gliadin ingestion. Despite genetic and epigenetic studies, the pathological molecular mechanism remains unclarified. The strong genetic component does not explain more than half of the hereditability; we identified several epigenetic features that contribute to the understanding of the missing hereditability. The lipid profile of infants has been proposed as a potential biomarker of CeD metabolism that can be measured before they exhibit developmental disorders and clinical symptoms. We suggest that the state of the host is a main factor for the abnormal immune response to gluten. Long before any exposure to the offending agent or any production of specific antibodies, several molecular mechanisms are differentially expressed in infants who will develop CeD compared to their peers matched for the same genetic profile. The present study explored the serum phospholipid profile of a group of infants at risk for celiac disease, followed up to 8 years to monitor the onset of CeD. We compared 30 patients who developed the disease with 20 age- and sex-matched peers with similar genetic profiles who did not develop the disease within 8 years. Serum phospholipids were analysed at 4 months, before exposure to gluten, and at 12 months of age, when none showed any marker of disease. In the 30 CeD patients, we also analysed the serum at the time of diagnosis (>24 months). The serum phospholipid profile was fairly constant across 4 and 12 months of age and, in CeD, up to 24–36 months. The phospholipid signature was dramatically different in infants who developed CeD when compared to that of control NY-CeD (Not Yet developing Celiac Disease) peers. We identified a specific serum phospholipid signature that predicts the onset of celiac disease in HLA at-risk infants years before the appearance of antibodies specific for CeD in the serum and before any clinical symptoms, even before gluten introduction into the diet at 4 months. Specifically, lysophosphatidylcholine, phosphatidylcholine, alkylacyl-phosphatidylcholine, phosphoethanolamines, phosphatidylserines, phosphatidylglycerol and phosphatidylinositol were found to be differentially represented in CeD versus NY-CeD. A set constituted by a limited number of alkylacyl-phosphatidylcholine and lyso-phosphatidylcholine, together with the duration of breast-feeding, allows the discrimination of infants who develop celiac disease before 8 years of age from those at a similar genetic risk who do not develop the disease. In addition to recent discovery, our paper unveiled a specifc phopholipid profile, able to discriminate infants who eventually develop celiac disease years before antibodies or clinical symptoms ensue.
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Affiliation(s)
- R Auricchio
- Department of Translational Medical Sciences, University of Naples "Federico II", Napoli, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Napoli, Italy
| | - M Galatola
- Department of Translational Medical Sciences, University of Naples "Federico II", Napoli, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Napoli, Italy
| | - D Cielo
- Department of Translational Medical Sciences, University of Naples "Federico II", Napoli, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Napoli, Italy
| | - A Amoresano
- Department of Chemical Sciences, University of Naples "Federico II", Napoli, Italy
| | - M Caterino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Napoli, Italy.,CEINGE, Biotecnonologie Avanzate s.c.ar.l., Napoli, Italy
| | - E De Vita
- Department of Chemical Sciences, University of Naples "Federico II", Napoli, Italy
| | - A Illiano
- Department of Chemical Sciences, University of Naples "Federico II", Napoli, Italy
| | - R Troncone
- Department of Translational Medical Sciences, University of Naples "Federico II", Napoli, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Napoli, Italy
| | - L Greco
- Department of Translational Medical Sciences, University of Naples "Federico II", Napoli, Italy.,European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples "Federico II", Napoli, Italy
| | - M Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Napoli, Italy. .,CEINGE, Biotecnonologie Avanzate s.c.ar.l., Napoli, Italy.
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KhalKhal E, Razzaghi Z, Zali H, Bahadorimonfared A, Iranshahi M, Rostami-Nejad M. Comparison of cytokine and gene activities in tissue and blood samples of patients with celiac disease. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019; 12:S108-S116. [PMID: 32099610 PMCID: PMC7011060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AIM The aim of this study is to explore the expression of genes associated to celiac disease (CD) in the target tissue and peripheral blood monocytes (PBMC) or serum to introduce possible potential biomarkers. BACKGROUND Celiac disease (CD) is an autoimmune disease induced by gluten ingestion in genetically predisposed individuals. Despite technological progress, small intestine biopsy is still the gold standard for diagnosis of CD. METHODS CD data were collected from public databases (proteomics and microarray-based techniques documents). Differentially expressed genes (DEGs) in PBMC or serum as well as small intestinal biopsies from celiac patients compared to normal were collected and analyzed to introduce common individuals. Gene ontology was done to identify the involved biological terms. RESULTS Among 598 CD genes in biopsies and 260 genes in PBMC or serum, 32 common genes with a similar expression pattern in both sources were identified. A total of 48 biological terms were introduced which were involved in the CD via the determined DEGs. "Cytokine activity" was the most expanded one of the biological terms. CONCLUSION In this analysis, it was concluded that 32 potential biomarkers of CD can be assessed by complementary research to introduce effective and available biomarkers in biopsy and blood.
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Affiliation(s)
- Ensieh KhalKhal
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hakimeh Zali
- Proteomics Research Center, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ayad Bahadorimonfared
- Department of Health & Community Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Iranshahi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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